problems with a 2.0 16v swap into a 84 Jetta GLI

A friend and myself did this swap. Not our first, but it was different. '92 Passat 2.0 16v was donor, bottom end rebuild, not the head (all looked good, this may have developed the prob) . Used existing CIS (jetta), with scirocco upper intake and exhaust manifolds. Changed throttle valves for one with a switch setup for knock sensor ign. Put in Knock sensor setup from 86 GTI, set it for 6 deg adv, worked good for some time. Vacuum was a problem, I think it may be ironed out now. Current Problem #1: variable idle, may be related to idle stablization valve (not used with this CIS) or Aux air reg (CIS); #2: a miss may be ign or fuel.