New motor in and pair valve trashed, 2 pair tubes plugged and small vacuum looking tube on front carb is plugged(I think it went to the pair valve). It seems that now the idle is not constant. WTH? What causes this?

 

Have you synced the carbs? Are all vacuum lines connected or plugged? PVLIR?

An engine swap is a pretty big operation. Double check everything involved with installing the carbs and airbox. Make sure the large opening under the right rear of the airbox is sealed. I used a 5/8" coolant bypass cap and a zip tie, bought at the auto parts store.