Recently swapped a t56 in my car and went to the JY and picked up a spare vacuum switch from another 3rd gen w/ cruise.
I put a "T" on the vacuum line and ran it to the 2nd switch. Also wired the plug in series with the original vacuum switch.

Depressing the clutch does not deactivate the cruise settings, however it releases the throttle (wont redline the engine). When the clutch pedal is released, the cruise goes back to its previous settings (MPH goal) and all is well.

I am really pleased with how it works, you can shift gears without having to deactivate the cruise.
Does this sound about right or did it work differently from the factory?

I only ask this questions because I had thought that it would disengage the cruise totally like pressing on the brake pedal.

This is the switch I used

 

I had an 87 TA 305 tpi 5 speed with Cruise and when I depressed the clutch the CC would disengage completely.

The T56 should have nothing to do with how the CC operates. I'm wondering if you wired it up wrong. Its a nice feature except for one problem....if you have the CC set and are on a road with traffic light or traffic and you re-engage the clutch while slowing down, while the car start to accelerate? That could be a dangerous situation for you.

My 00 TA disengages the CC altogether when the clutch is depressed. While that sucks when changing gears at highway speeds, I would prefer to just press the "Resume" button then having to remember to shut off the cruise before engaging the clutch again in a decelerating situation )traffic, stop light, exit, etc)