Putting one of those small dry element filters on it is going to cause what could be described as a whistle. nothing to do about it other than try a different type of filter, usually a larger one. If you have an oil bath filter handy, you could try that to see if it changes the sound.
Checking the compression would be to see if you blew the head gasket between cylinders. This usually causes a ping under load, rather than a whistle, though.
If your timing was off, it would also cause more of a ping than a whistle as well.
It's possible you have a vac leak, but it would give you other symptoms as well, like a lean backfire on deceleration, or a rough idle, or surging, for example.
It sounds to me like you are leaning on it a little harder then you used to because you went from a 3:90 to a 3:36 gear, and the type of air cleaner you are using. I'm not sure I can pin it down any better without being there or at least hearing it.
