The spark is controlled by the flywheel. See the little square tab on the side below? That passes under a pickup coil similar to a tape head. That creates a signal that goes to the ECU which generates a spark every revolution. Both at TDC. One of them is wasted.
So its pretty much impossible to mess up spark timing. The cams are probably correct as well because if they were the source of your problems, you would either have valve-piston collisions or backfiring. Just make sure you set IN and EX with the crank on TDC for cylinder #2 and not #1.
Did you take the heads completely off - exposing the pistons?
If you have it back together now, I don't see the point in removing the heads.
If you have spark, and still can't start, the carbs are the usual culprit. It may or may not be possible to start using starting fluid. I've never been successful doing that, but others say they have. With the bike sitting during repairs, the carbs are probably clogged.