Did the sustain work before cap change? C6 a 2.2uF cap is in the sustain circuit. Make sure you did not swap it with 1uF or 100uF.
Kiss and Star Trek use different ROM and jumper, but it should still kind of work in both games. One game may be missing an input coming J1, but again i would not expect it to "squeal" constantly.
Bally's own repair guide is pretty good for this board.
http://arcarc.xmission.com/Pinball/PDF%20Pinball%20Misc/Pin%20Repair.pdf
Also check out the repair notes by Oliver, also very good. Oliver uses a scope, but most things in his diag process can be d one with a logic probe or even a DMM.
http://www.pinball4you.ch/okaegi/rep_soundold.html