Matt, I can stop by your house to give your PCM an update and see if it helps with the cold idle surge. Did you get that misfire solved?
I've sent another PCM to Brent as well, hopefully it will fix his idle surge.
The issue has to do with the timing advance just above idle. I increase the timing advance in the 1200-1400 rpm range for vehicle cruising to increase the gas mileage. There are separate tables in the PCM (hidden in most tuning softwares but they're there) that have separate timing advance for idle, but they are not enabled until the vehicle warms up; when its cold, the PCM uses the main timing table, and if the high idle at first startup hits the increase timing advance mentioned above it will cause the idle to surge and then fall and repeat as the timing advance changes. Putting into gear lowers the rpms and creates some resistance against the motor, one of which or both is enough to stop the surging.
There's no harm being done but I realize this is 100% annoying.
The fix has been to increase timing advance at idle, decrease the cruise timing advance a little and so the timing stays more consistent. Whenever possible, I have enabled the idle spark tables at low engine temperatures so it uses that table (as it should) rather than the main table, thus being able to keep the higher cruise timing.