Most of your questions can be answered by using the search feature. But, off the top of my head...
L series (six cylinder) heads are all swappable. E88, E31, P90, P90a...if it's for a L24/L26/L28, you can put it on any of them.
390 is probably more than enough for a little L24.
the KA 5spd will not bolt to the L (AFAIK). If you want a five speed, you should start looking for a L specific one (they're pretty cheap though, so it won't be hard).
as for overboring an L24, why not just use an L28 in the first place? or if you're really set on using the stroke of a L24, just swap a L24 crank into a L28 block.
As for the questions re S13s...probably going to be better off asking on a different forum. People here are generally going the other way with engines.