Keep it simple! It's a Yamaha not a Taiwanese. I'll admit weird things do happen, but not very often. Fuel, spark, and compression is about all you "should" need to check for. If you have good compression and it sparks you still have a fuel/carb problem.
A compression test will tell you if the valves are tight. If you don't have a gauge put your finger over the spark plug hole and turn it over. If you can't hold your finger on the hole it's probably alright.
I would clean the original jets and put them back in. The aftermarket kits sometimes have different size jets with the stock number stamped on them. Poke them out with a strand of wire.
