I'm new to KI. I tried performing a manual combo on practice with Thunder, and sometimes I would get around 40% while other times I would get 77?! Sometimes I would get 15 hits, while others (holding the last button I pressed, the fierce punch, for the ender, it seems) I would get 16. What's that?

Whenever you don't end a combo with an ender, you leave "white life", or potential damage, on the dummy character. So if you drop a few combos in a row, then finally end one, the dummy will have a ton of potential damage that gets erased by the ender, and the damage for your combo is higher than normal. If you are testing damage numbers, make sure that there is no white life on the character first! You can wait for it to regenerate, which is fine if there is only a small amount, but if there is a huge amount of white life, you can just do a short combo + ender to get rid of it more quickly.
Getting more hits on your combo is because enders hit more times if the ender level is high (and ender level is directly related to the white life your opponent has). So, sometimes you were getting a level 3 ender (3 hits) and sometimes a level 4 ender (4 hits), because of the white life thing I explained above.