1.) In NEC I don't see that you need to account for the 20a bath circuit in addition to the general load calc (3 VA / sq ft) is that correct?
That's correct. For kitchen and laundry, all the 20A circuits dedicated to that room get allocated 1500 VA. The dedicated 20A circuits to bathroom and garage do not require a 1500 VA allocation, and are simply counted in the "3 VA per square foot of habitable space" catch-all.
So if Joe decides to install four kitchen and two bathroom receptacle circuits, exceeding the slumlord bare minimums... then Joe counts 6000 VA (four kitchen circuits x 1500 VA and none for the bathroom). I.E. the number of actual circuits is what counts.
Also note the 20A circuit for garage and laundry are not exclusive the way kitchen and bathroom countertops are. As long as laundry and garage have the one statutory 20A circuit, any random circuits* can also serve those spaces. Code is fine if the washer is served by a bedroom circuit and dryer is on lighting circuits, with the mandatory dedicated 20A circuit serving only a Febreze lol. That's relevant to garage; my strong reco is to have the mandatory 20A circuit serve only one receptacle - positioned to be viable for EV charging. That way it can be trivially converted to 240V for 3.8 kW charging, which will take care of almost all needs for almost everyone (for the exceptions, DC fast charging).
2.) My standard NEC calc, if correct comes to 161a, which is very high (most due to EV and Hot tub), did I calculate this correct? (I included the hot tub and EV and new garage circuit at 100% and add 1.25 safety multiplier, is that correct?)
You have to be careful with the multiplier there not to apply it twice. That has to already be accounted in the size of the circuit breaker. So a hot tub or EVSE on a 60A breaker can only draw 48A actual. Thus a 60A/14400W circuit is providing 11.5kW EV charging, which is the hard max for most EVSEs, and more than most cars can even use*. If you wonder how the car has a say in it, see this.
Everyone's expecting me to give a big lecture on 60A EV charging not being necessary; I'll let Technology Connections do that. But hey -- if you're building, and have a blank-sheet number where you can write any number with no interlocking consequences, why not? It's bonkers for one EV, but get 3 or 4 (or 2 and a time-of-day tariff) and suddenly 60A on Power Sharing just makes a world of sense. Power sharing lets a group of EVSEs share a single current allocation, so if only 1 car is charging it gets the max, otherwise it is split. This calculates on the fly because of EV charging magic.
By "magic" I mean that this is SAE's 4th major attempt at an EV charging standard, and it wasn't designed to sell service upgrades. It was designed to sell cars :)
And yes, it's a standard. Tesla uses it with a different shape connector, and Europe does the same (the shape accommodating two more phase wires, but same protocol).
Note also that "Grid Limiting" is an EVSE feature that allows you to ignore the Load Calculation. It puts a clamp ammeter on the service or feeder wires and tell the EVSE "don't let the feeder amps exceed 80" and it will throttle EV charging accordingly.
When commissioning an EVSE you generally set the breaker size via DIP switches or equivalent, and it automatically figures out the 125% for you (e.g. on a 25A breaker it tells the car to take 20A actual).
* You might think "Oh, as the EV market matures, AC charging will get faster" - nope, they're getting slower. a) EVs aren't luxury anymore, and large chargers make the cars costlier and heavier. b) field data is showing high power AC chargers rarely make a difference. And c) DC fast charging is proliferating, with prices falling - expect home models for "I want the Fastest Charge Possible" types. This is the best of all worlds, and what most people thought they were getting all along.
3.) NEC Alternate method (200.80) comes in significantly lower at 95a. Is this method allowed for my case? Did I calc this correct? If so, with such a difference, even though it may be allowed, perhaps it is not feasible as it will cause frequent tripping?
The deal there is, there's only one NEC. So the standard method has to accommodate everything from laundromats to nuclear power plants. The alternate method is simplified for residential dwellings.
4.) I'm currently not including the 2 circuits I need to move from the existing sub to the new sub. They are partial 2nd story lighting circuits...how do I add those loads to my calcs?
If they serve general lighting or appliance loads that aren't assigned as part of an appliance's calculation, then they fall in the "3 VA per square foot" part of the calc. So the square footage served needs to be allocated to the subpanel.