Custom chip & PMS possible?

I have a quick question. I installed a Vortech SQ, Trickflow heads, Performer intake, 80mm Pro-M, 70mm BBK, 42 lbs injectors on my otherwise stock shortblock. I purchased a Anderson PMS to tune it, but I am fighting getting it to idle and run well. I have been looking up past threads and have done what I can do, but I just don't have the time with everything else in life to keep trying. I contacted a local shop that has a dyno and said they would burn a chip for it, but would not tune it with the PMS. If I were to have them do this, could I still keep the PMS installed to make changes from that tune as needed in the future? I don't see why not being a piggyback unit, but wanted another opinion. Thanks for your help!

Well, one problem I have is that I don't have a wideband, so I am only going by what the stock ones are showing. Here is what it's doing. When it is cold, it will start and idle fine at around 740rpm. Once it starts to warm up it will start to wondering from 950rpm to 650rpm. The main driving problem I am having is once I take off it will run ok until the first hill I go down with my foot off the gas. This will cause the check engine light to come on, then I will push in the clutch to stop and it will just die. It will restart, but runs bad after that (limp mode maybe?) The codes are MAF below min voltage and TPS higher than expected. I talked with Pro-M to make sure I have the correct MAF and they said I do, but I put my stock MAF and injectors back one and it ran fine (slow driving of coarse). He said the throttle blade may be closing to much and not letting enough flow through the MAF. I have re-set the idle by what I have found in other threads, but it still doing it. I have tried clocking the MAF, changing around the plumbing after it to smooth out airflow, and adjusted the tps to .98volts. When I first put this all together I had the same problem and the car surged bad going down the highway. Rick Anderson said to add fuel and see if it went away. It did help. I kept the stock cam in hopes that I wouldn't have these problems, but I have been fighting this thing for almost a year (just hard to find time) and I am ready to start driving this thing regularly again, thats why I thought maybe this speed shop could get it right with the custom chip and then I could still make changes with the PMS as I change the car, but it was just a thought. Does anyone know a shop (or individual) in the Kansas City area that can tune it with my PMS?

Thank you Redsnk95 for your help. It is a Series IV. I do have the tps setting to read idle. I believe the start up is around -20% right now. I will watch the O2's more carefully. They seem to be going rich / lean fairly quickly, but I will watch closer. I have played with the air adjuster, but will continue that also. Very interesting on the water temp table. I had not dug into it enough to know that the temp can adjust the startup fuel. I did find a local shop that will tune my setup with the PMS and it's going there next week. Hoping they will get it right on and curious to see what numbers it will put down.