My question about tapping the lines was this: I added wires in place of the optics on the mouse. To make sure everything is still okay with the mouse, can I touch some of the wires together to simulate the wheel spinning in the optic sensors? For example, can I touch the X1 and X2 wires together repeatedly and the mouse pointer move left or right in my test program? Or is something like that not possible.
I didn't remove the transmitters because I thought it was unnecessary (I only removed the receivers where I soldered my wires instead). I will remove them and see if it helps.
You're safe leaving the transmitters on, right.
Touching the wires together isn't really going to do much. Here's how bidirectional optical encoder signals look:
X1 ----____------____-----
X2 ------____------____--
reverse X1, X2 waves for opposite direction.
Connecting the wires together won't really do much.. what you could try is hooking two switches up to the 2 inputs on the mouse so that pressing it switches from 5V to 0V. You could alternately press the two switches in the pattern shown above to test the mouse board. Although, the pointer will move very very very slowly

Basically the mouse uses one of the lines as a clock, and on rising edges, of one line, if the other line is 1, then direction is left, if it is 0, direction is right (or vice versa, depends on the hardware). The number of clocks indicated the amount of space travelled.
My biggest problem recently was just trying to figure out which 2 of the 3 pads from the old receiver to use. Trial and error, only 3 possibilities really. Of course, it was a different footprint between 2 different mice. You may just have the leads on the wrong pads.
Hope this helps.