It's the con of swapping a 1G into a 2G bay. The 2G crank and cam signals are separate sensors and therefore higher resoluation than the 1G CAS combo. Any minute stretching of the Tbelt can cause a problem along with several other variables.
There is a few things to do, among them is buy the Kiggly crank sensor.
Kiggly Racing - kigglyracing.com
Or this list of stuff from RRE
How do I get rid of the Random Misfire studded and check engine light?
RM (Random Misfire)The ECU is flagging a misfire condition because the crank
sensor which originally drove the hyper accurate signal for the 2G ECU has now
been replaced and simulated by the not so accurate 1G CAS. The only remedies
for this symptom once you have it is:
1. Start over again and do it the original RRE way by modding the oil pump case
and keep the crank signal. RRE does not do it this way anymore, so why would
2. Wire in a potentiometer on the barometric sensor wire going to the
ECU,thereby fooling the ECU into thinking you are at very high elevation (low
barometric pressure) so it doesn't check for RM. This sounds simple, but if you
don't tune the engine to compensate for the additional timing, you will end up
turning your piston's to goo which also kills your turbo. (Not a recommended
3. Cutting the TPS sensor wire. This actually appears to work for some
people,but since TPS is useful for data logging and tuning, its not a good long
term fix. This may also effect engine performance during times when the ECU uses rapid changes in throttle position.
4. Buying DSMLink and clicking a tiny little checkbox which basically disables
the ECU logic that checks for RM.