Very interesting and well thought out.
Its totally doable and for and ecu, i would be looking at a late model engine and use the ecu from that.
As for the oil drain, and you can always drill a hole and tap a thread to take a fitting to drain it back to the sump. that’s no biggie. Neither is having to block thins off. I have done a similar thing with putting a blue motor 12 port head onto a red motor bottom end and visa-versa . Had to drill holes int he block to accommodate steam holes and just bolted the head on to block any water galleries not needed. Never had any issues with it. And I cant see any major problems with your ides.
There’s plenty of people here to help you out .
AS for the cams an firing order, it would be the same as the bikes.
There’s only a couple of ways to set the piston order. If they are in the same order, ie the two outside go up while the center 2 go down, or 1 and 3 go up while 2 and 4 go down
As long as the piston order is the same your right to go. If you need to move the stud position, you get a bolt, locktight it into the block where you need to move the stud, let it set and lop the top off with a cutting disc. Done right it while be close to invisible. You can then re-drill and tap the hole in it’s new position, and can cut into the blanked hole.
Cheers, The Prof