I describe my alternate approach at the bottom of this answer
In terms of the picture in the original post ...
For the drip cap, I'd cut it long, then fold it upwards and forward, snipping along its bends to make this possible, then caulk the outside and backside of the corner, and 12" along the top of ledger. The drip cap can serve one or two purposes. First - and essentially - it acts as feathering to prevent water from getting behind the ledger and possibly into the house. Second - and optionally - if it projects out past the ledger (say 2" away from the house), it acts as a drip edge, keeping water from running down the outside face of the ledger.
For the upper undersill trim, I'd cut it long and bend it down over the j-channel.
For the z-flashing, I'd work it the same as the drip cap, and have the J-channel lap over it on the ledger side. Also I'd have the house wrap lap over the front of the z-flashing ... but if this required cutting the existing house wrap along the length of the ledger, I'd leave the existing house wrap intact and put on 2nd layer, roughly 2x the width of the ledger, slipping the new sheet of house wrap up under the aluminum/vinyl siding as much as possible.
For the joists, I'd notch them on top near the ledger so that drip cap remains continuous, slanting each notch to the side, making sure the top of the notch was smooth.
For joist hanger nails, I'd make sure they were shorter than the thickness of the ledger so that they did not puncture the house wrap.
For the ledger bolts, after predrilling, I'd caulk around each hole on the backside of the ledger, then tilt the ledger up into place and secure with bolts.
For the ledger, I'd keep it 1/2" - 5/8" up off the z-flashing. I'd also put a small chamfer on the back of the butt ends, then caulk that back corner. I would not worry about the the front of that joint (between the butt end and the j-channel) being caulked.
For the deck board against the house, as @Jacob commented below (I think), I'd cut a 1.5" x 5/8" bevel on its underside along the edge that is next to the house so that it does not bear on the drip cap. Alternatively, especially since you indicated in the original post that you will be custom bending the drip cap from coil stock, the top edge of the ledger can be beveled away from the house, contouring the drip cap accordingly. Either way, I'd leave a 1/4" space between the deck board and the drip cap.
If it is compatible with the house wrap, my choice for this type of caulking is butyl because it remains soft and flexible. It's extremely messy, but not more than a roll of paper towels can handle.
Personally, though, I'd install the ledger in an entirely different manner. I'd gently remove the relevant courses of siding, keeping them intact. I'd then fill-in their backsides with DIY shape-matching pressure-treated 'clapboards' cut from say 1x4 or 1x6 PT, then reinstall the bolstered siding. At this point, the house will look just as it did before. Then at each bolt/screw location I'd install 6" lengths of similar PT 'clapboards' upside down against the siding. These 6" lengths will create a flat and vertical surface. At each of these locations, I'd install a scab of pressure treated DIY cut to 1/4" to 3/8" thickness, 4-6" wide and length equal to the width of the ledger, installed with the grain running vertically. The scabs will hold the ledger away from the siding to allow for drainage. The tops of the 6" lengths and the tops of scabs ought to be tapered left and right to promote runoff.