Check simple things first. Spark plugs, vacuum hoses, clean linkages, clean and tight connections to the coils, spark plugs leads, TPS, etc. Any of these could cause the problems you describe.
Check all battery connections, including the other end at the starter motor for cleanliness and tightness. Be especially careful at the starter motor as it is easy to get a big spark if you get your tool too close to the wrong thing.
Don't forget, and it's easy to do when you are frustrated, to check that the kill switch is in the correct position.
There are 2 types of bikers, those who have forgotten to turn the kill switch on, and those who won't admit it.
Is it possible to get replacement keys?
Some models have an extra "key off" on the LHS of the bike. If it has that, and it is turned off, then that could be a big part of the problem.
I hope you haven't removed the secondary TPS, but if you have, then you can't just put it back on. You will need to open the butterfly and attach it with them open. Sort of back to front from the primary TPS. You will need to do this even if the butterfly valves have been removed.