OK, this sounds like my car for the last several years, especially the surge-drop issue. I took it to every tuner you can imagine, including Granite State and Performance Dyno and no one could really cure it, though Alex at Granite State did the best job. But it's mostly gone now. What did I do?
First I used some MAF cleaner and replaced the EGR valve (not your issue, obviously), it got a bit better. Then I replaced the IAT and CTS and it got a bit better. Then I put on a new dizzy cap, rotor, and made up a new set of custom length wires from the Moroso Blue Max kit (since I found some of the FRPP wires too short and getting fried and arcing to my equal length shorties). Now the issue is almost gone. It wasn't any one thing, just a bunch of little things that were getting too old I guess. You can't tune your way out of that. Total cost of all of the above (excluding the EGR valve) was unser $200 - cheaper than a tune.
BTW, don't worry about the bad memory in the ECM issue. Almost every custom tune out there will get that. It really means that checksum on the memory failed. This is not surprising since the code is different and it would be a one in a million chance that the checksum would be the same. I have heard that the checksum can be changed, but since the error is a "soft code" most tuners either don't bother or don't know how to do it.
As for tuners, did you try Dez in Seekonk?