This is a super hard problem, because you are renting and seem to be "at war with" with your landlord and AHJ, rather than working with them. That's a shame, because what you want is reasonable and it should be possible to get all to agree to it.
What you have done so far puts the landlord in a no-win situation: he absolutely must positively end the practice by shutting off the power and evicting you. If he does not, he becomes liable for it just the same as if he did it, for lawsuits if anyone is injured, and if the city finds out, fines and paying a pro to rip it out and search for any other gypsy work. Meanwhile, if the city gets wind, they will condemn the occupancy and again you will be evicted. The landlord might even "drop a dime" so the city is evicting you (not him) and to avoid the fine. Any costs for him would come out of your deposit.
That said, I think a proper generator inter-tie is something most tenants would find valuable. So from the landlord's perspective, he has a more marketable property if it is so equipped. So there is certainly room to work out an agreement. In your shoes that is what I would seek to do.
Of course all work would have to be to Code and inspected. Depending on the jurisdiction, it might have to be hired out unless the AHJ recognizes you as qualified to do the work. I assume that would zorch the deal. But you don't know 'til you ask. I suspect outside the big cities, where everyone is just trying to get along, the AHJ may abide reason.
Do keep in mind that all tool-installed modifications become property of the landlord the moment you install them. You must do good work because it is electrical, but you must also be prepared to leave it (intact) for the next tenant when you move. That is the price of being a tenant, just like having to suddenly drop $2000 on a furnace is not.
Many ways to get a generator interlock when you don't have one:
Convert each load to be cord-and-plug connected
And just run an extension cord to it.
For instance your furnace wiring probably ends in a simple $1 Handy-Box. Stick another one 3" away from it, and use the furnace wiring to fit a receptacle there. Then add a short cord with proper strain relief coming from the furnace which, you guessed it, plugs into that receptacle.
Power failure comes, run an extension cord down there and do the obvious.
This is Code legal because Code allows utilization equipment to be cord and plug connected for special applications like this.
This will set you back about $10 per circuit.
On each circuit, add a DPDT switch
A DPDT (double pole, double throw) switch has 6 screws and has an A side, a B side and a common. It's a mini transfer switch and costs about $10.
find an appropriate location along the circuit where this will be possible. Wire the common on the DPDT switch to the downline circuit, the "A" is wired back to the service panel, and the "B" goes to an inlet. Or alternately, wired to a subpanel exclusively powered by the generator.
Switch both hot and neutral.
The trick to wiring this is you lose about 18" of wire with the 9" of wire that needs to be inside the box so you can work on it... so you need to make that up somehow. You can do this near the service panel or a load and simply replace the now-too-short section. Or you can put two boxes 18" apart, and have a 3' jumper between the two boxes. The second box can be a good place for the inlet.
I know I went real fast by the part where the generator has a cheapie subpanel all its own. This can be a tiny thing, it is just to provide correct overcurrent protection for each branch, e.g. A 14 AWG-wired branch needs 15A breaker protection. Or you can use inlets and extension cords to the sockets on the generator.
Install a subpanel with onboard transfer switch
The general idea here is that you install a new sub-panel near the main panel (or wherever else convenient). You then take each of the circuits you want to power off the generator, and permanently relocate their hot, neutral and ground (the whole cable really) to the subpanel.
This type of subpanel has a "sliding piece of metal" interlock which prevents both the utility supply breaker and a breaker in a very particular location from being on at the same time. Obviously, you put the generator backfeed there.
Where it differs from the "retrofit this" example that I moved from the bottom, is that in this case, the manufacturer has engineered the whole kit-n-kaboodle to work together - subpanel, breakers and interlock - so it costs far less. It fits the breakers and the breaker bolt-down feature (discussed below) is present. Often the top 4 spaces are occupied by two 2-pole breakers; and a simple bit of sliding metal sits between them. It's super simple and easy to understand.
Yeah, but with a lot more spaces.
This is big-box's offering. A real electrical supply house should have much better options.
As always with subpanels, spaces are cheap, so don't scrimp on the spaces. 30 is not excessive, running out of spaces is seriously frustrating. With 4 used, that leaves you 26 spaces to put loads on. I myself would go 42, but I'm crai.
The tie from main breaker to sub should be the biggest wire-breaker match-up you can stand to pay for. The breaker in the main panel must match the wire you are using since it protects the wire. The breaker in the subpanel is really just there to be a cheap high-current switch.
The breaker on the generator side should be sized for the generator, unless the gen has its own onboard overcurrent protection, in which case again it's just a switch.
When moving a circuit, if it doesn't reach, I simply put a large box where it and other circuits can reach - typically a 4-11/16 deep box - and bring the cable into that box, then extend the last few feet to the new sub. I do this all the time for other reasons. Use good wire-nuts (Ideal) and nut quite firmly (it is one place "gorilla tight" is appropriate). I've never had a splice problem.
When using the subpanel, simply cut all the breakers off including the interlocked main breaker, hookup and start the generator, turn the generator-side main breaker on, and throw on circuits one at a time as desired.
A subpanel with an external transfer switch
This option may be more expensive since it isn't using $10 breakers as cheap switches. Or maybe; the above pictured "micro subpanel" would totally work as an external transfer switch. It certainly doesn't work as a subpanel.
This has one big advantage: you can switch neutral. That matters if it's downstream from a GFCI or AFCI, and many generators have integral GFCIs these days.
This is a large DPDT, or 3PDT (double/triple pole, double throw), changeover switch. You can use ones specifically made for generators, or ones made to switch 3-phase power. (neutral as the third "phase".) The point is they are double throw, so the "common" position is connected either to source "A" or source "B", and A never connects to B (hence the interlock).
A and B go to mains and gen; common goes to the new subpanel.
Made for 3-phase.
Again, a real electrical supply house will have much better selection and price. The switch, and the mains to subpanel wiring, should be as heavy as you want to pay for. The switch-to-gen wiring can be sized for the gen.
Here, you use a perfectly ordinary subpanel, with no special features needed. It can have a main breaker, or not. Then as above, you cut over to the new subpanel the circuits you want to have on generator.
An external automatic transfer switch
As the last case, ditto ditto ditto but with an automatic switch that senses mains power and cuts over to it when it's present and stabilized. You can also get switches which will auto-start the generator.
You can guess the huge gotcha: since you wouldn't be there to throw over circuits one by one, it slams all load onto the generator. That requires a higher "tier" of generator product, not a $1000 model with wheels but more like a $5000 job that bolts down to a slab and takes natural gas.
You can't do this, but for others...
Retrofit an interlock on an existing panel
There are several companies that make aftermarket interlocks for almost any panel. These work about like what you're doing now: you retain your existing main breaker, fit your generator backfeed breaker in a very specific location, and then they supply a sliding metal bracket which interlocks so the main and this backfeed breaker cannot both be on at the same time. Done and dusted.
There are two serious hitches with this: First, they don't make such things for every single panel, so it's luck whether your older panel is supported. (cooking up your own [that works] is far better than having no interlock, but it isn't listed, which means it isn't legal.)
The other hitch is a special rule in Code for backfed breakers, which is that they must be "bolted down" so they can't easily snap out (most breakers on most panels snap out) and nail somebody with their exposed metal bits. That requires a design concession in the panel. Or simply a panel where all breakers normally bolt down, such as some Siemens panels. (doing it anyway isn't legal, but again is far better than not having an interlock, can't tell you to break Code.)
What not to do: octopus "transfer switches"
You will see these multiple-circuit "transfer switches". They look like something out of an RV, very impressive with an entire row of 6-10 switches, sometimes breakers too. They are aggressively marketed, and all too easy to buy. However they are a nightmare to wire.
Because for each circuit to be put on generator, they require you intercept the circuit on the way into the service panel. Divert the load side to the box, divert the line side to the box also, so it can be on "A" and common on the switch (we're up to 6 wires so far), then also the wires to the generator. And that again for each of 6-10 circuits. It's crazy bunches of redundant wiring, hard to understand and unnecessary. But like I say, the generator salesman practically won't let you leave the store without one. He gets a commission on those hokey things and not on subpanels.
Not pictured: 52 wires going in and out of it.
The only nice thing these transfer switches do is allow some circuits to be on "line" while others are on "gen". I fail to see the usefulness of that. If utility is available, just use it.