I think your timing is off as well. Your differently getting fuel and if your getting spark at the plugs then the whole ignition system should be ok. Also check your plug routing, remember that cylinders 5 & 6 are swip swapped in the firing order. Also, did you be double sure to make sure you reconnected the CPS connectors? That would explain everything as well. If you did then I would suggest you do your timing again, it can't hurt. After doing mine a couple times I can manage to completely strip the acc. side, do my timing, and put it all back together in about 90 minutes..
my method is as follows :
Remove all spark plugs, usually one of the cams will sort of spring forward due to compression, as long as the plugs are out I found it's easy enough to use a rachet with a 10mm socket and turn the front cam gear using one of the 3 bolts holding the gear to the cam (in which ever direction needed) until it matches the other one in relative location of the notches. If your turning the cam gear more than 1/3 turn your probably going in the wrong direction or turning the wrong cam. Be careful here, it shouldn't take much effort at all.
At this point I put on the belt ( doesn't matter how you put it on at this point) and loosely tension it and turn the crank with the crank bolt and a 18mm rachet until the notches on both cams are at their respective TDC marks on the timing backing plate. Take the belt back off (cams shouldn't move now if they do just turn one that isn't at TDC back to it's mark with the ratchet again ).
Check for TDC @ cyl #1, cut a wire hanger into about a 30" straight piece, plumb said piece of wire into cyl #1 until it touches the cylinder, rotate the crank (with the belt off and the cams already lined up) until the wire is as high was it goes and then check to be sure the mark on the crank gear is in the vicinity of the notch on the block (about 5 o' clock ). Put the belt one with the lettering upside down from the point of view from the acc side of the engine, put the two line for the cams on the exact teeth they belong. Once you get the belt on you should be at either the 3.0l mark or the 3.2l mark depending on whether you have an ATX or MTX. If you did the 3.2l swap in an MTX then you want the 3.0l marks as they correspond to the timing covers used from the 3.0l.
I like to talk and help all I can, good luck!
BTW: cylinder 1 is in the rear bank closest to the pass fender..
-Josh