92 Gt Rough Idle On Cold Starts (long)

I know this is my first post her on stangnet, but I have been on the corral for years but I have finally got fed up with a few of the members there and am hoping to get some honest help and guidance over here. Ill try to make this as brief and informative as possible so that I can get all the info out there.

I bought this completely stock 92 GT from a guy that had given up on it and let it sit for years. When I got it, it had a lot of issues, mainly electrical and driveability issues, but most of these have been resolved but I can not fix the cold start idle issue that it has. On initial start up, the RPM's will drop to around 450-500 rpms, sputter for a few seconds and then climb up to around 1000-1100 RPM and then slowly make its normal idle drop to around 750 or so according to the factory tach. Along with that, the motor feels like it has a slight miss at idle or almost like it has a really small cam in it until it warms up and then everything runs fine. If it matters at all, the car also has an extended crank before it fires up on cold start as well. It does not stall or surge, idle holds steady around the 750 mark but it sounds like it has small cam in it. Another thing to note is that on start and go situations, the car bucks a little backing out of the drive and then while coming out of the neighborhood. After a few minutes of driving, car runs great and idles smooth as could be.
Dumped codes and I get:
KOER
31 EGR Position Below Minimum Voltage (EGR has been removed for diagnosis and not reinstalled yet)
44 Secondary Air System Inop (all smog stuff is still hooked up)
94 Secondary Air Injection Inop (all smog stuff is in place)

KOEO
31 EGR Position Below Minimum Voltage (EGR has been removed for diagnosis and not reinstalled yet)

Cylinder balance test passed

Performed a compression test and all cylinders are between 130-145psi cold and dry.
Vacuum gauge shows a slow but rhythmic bounce between 17 and 16 in/hg

Like I said, this car has had a lot of issues and while fixing other problems, lots of things have been replaced. Here is a list of everything that has been replaced.
Computer (caps blown internally)
fuel pump (walbro 110lph), filter, swapped injectors, sending unit and cleaned tank
distributor (cardone), tfi (motorcraft), coil (motorcraft), wires (ford racing), plugs (autolite)
battery cables, TPS (motorcraft), ECT and ACT Sensors (both SMP)
IAC (motorcraft), BAP (motorcraft)
Replaced Vac lines, TB gasket, upper intake gasket

I have checked timing and it is set to 10*. Spray and smoke tested for vac leaks and found a small leak at TB. Replaced gasket. No change after that. Check fuel Pressure at the rail and its about 39 psi. Cleaned 10 pin connectors, cleaned Maf, cleaned TB. I also checked my new ECT sensor by heating it up on the stove, checking it out of the freezer and at various normal temp situations and the sensor is good (I was leery due to it being aftermarket).

Any ideas of things to check would be appreciated. I talked to a co-worker that worked in a ford dealership through the 80's and 90's that said they had a few issues with the vacuum solenoids in the smog system causing a vacuum leak basically. Not sure how to test that theory with out removing all the stuff and plugging the back of heads. Again, any advice or direction would be greatly appreciated.

I have used the surging idle checklist to get to this point and it has gotten the car at least driveable. I will go back through it again but one thing I noticed is it refers to a good cold idle but a surging warm idle. That isn't really my case. My idle is rough when cold and gets much better when warm. Like I said, I will go back through the list again though just to make sure i didn't miss anything.