Hi, I have just put in a "new" 4wd Engine in my Sapp. Cos, and have passed 3500 problemfree km.......but now it has developed a problem

.
It starts fine from Cold and idle is sometimes ok for 5-10 sek (still cold), but then it can start going up and down in rpm ( 400-1100rpm), and then back to almost normal and back again, also when trying to go it will sometimes stall or even when putting on the light it sometimes drop the rpm or also stall........when getting warm it seems to settle at around 800 rpm but with
some misfires...if stoping in trafic or after a run it sometimes idle ok for 5-10 sek and then the
misfire is back 
.
And when driving on boost and some load it seems to be ok, but on "part throttle" (no load) there is some small Hessitaion/misfire and when lifting off (engine braking) you can
really feel some Hessitaion/misfire !!!
I have new ACT, CTS, TDC, TPS, plugs, leads, gp A coil....and the car is running 4wd engine, 4wd loom with 2wd ECU and TPS (wires are reversed

), Ahmed Bayjoo stage 3 chip, 803's, 3 bar map and so on.....
So can anybody give me some good advice where to start....