Code Problems
 

I just put the VX transmission in my HX and for the past 1,000 miles I keep getting codes P0303 (#3 misfire) P0304 (#4 misfire) P1300 (Random Misfire), and P0000 (dont know what this means). I have had no codes before I installed the transmission.
I have checked all connections they seem good.
I was thinking about timing the difference. D15Z1 is 16 btdc and the D16Y5 is 12 btdc

Any indication why this would be happening

Did you touch the distributor at all during this swap?

The transmission has nothing whatsoever to do with engine timing.

It's possible with the tall gears of the VX tranny you're lugging the engine causing the random misfires. Are you trying to drive in 5th gear below 35 mph? That could be your problem. The final reduction gear ratio of the differential in the S20 is 3.25 and the VX 5th gear ratio is 0.702. The OBD II system detects and reports misfires the OBD I cannot.

What kind of scan tool are you using. To diagnose your problem adequately you will need to get a real time scan gauge - not a cheapo model under $100.

Like I said I checked all the connections.

I am using my Scan Guage II.

I am trying to avoid the lugging of the motor, but I used to lug the motor with the old transmission.