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On a 3 button mouse...

Is it possible to replace the IR receivers from the xy axis's, with a rotary encoder from the scroll wheel?

Is it just a matter of removing the IR receivers and putting in scroll encoder dials from other mouses?
Now on top of that same idea, can you use pots instead of the rotary scrollers?

I cannot find a pinout from a scroll wheel or a IR receiver anywhere...one of these would be nice also.

The mice I'm speaking of are the early type non lit underneath.
However a workup of both types wouldn't hurt as this will help with the newer stuff.

End result being able to use 3 separate dial axis and buttons from one HID mouse board.?

No you cannot easily interchange an IR with rotary encoder. Each uses a different set of electronics to support them and translate what the sensors pick up into the motion of the device.