If you're just barely touching the pedal (not really disengaging the clutch) and you hear a funny noise, to me I'd sure be pondering the throw-out bearing. Some of the new repop ones are of very poor quality. That would be the first thing I'd check.
Also, does the noise change or STOP once you push the pedal a lot further in? Sometimes a throw-out bearing will make a noise when it first starts to touch/turn, but then it changes once real pressure is applied - can be another kind of clue.
Also, how much did you have to grind on the flywheel bolt heads? If you had to grind much at all, then I would NOT be using that approach - get a new/different clutch disc. and replace the bolts.
The last thing you need is a failure of bolts on the flywheel - can cost you your legs. Not trying to be an alarmist, just that when you do things like this as a result of having the wrong part in your hands, it kind of worries me. (And we've all done stuff like this at one point in time).
Also, once your clutch disc wears out a bit, then the springs will probably be hitting your bolts once again.
Good luck!