Wanted to thank everyone that has help me try to get this thing running correctly. I like to follow up on threads I start so it may help someone with similar issues. Well I hope it helps and doesn't confuse them more.
Due to work and weather I haven't got a log worthy of posting though after much testing/tuning I have the stumbling and surge completely gone "for now". As mentioned these issues popped up out of nowhere that I can't explain but ohh well that's the way it is.
Lionel was correct as well as what Steveo mentions on his page about INT Delay and I doubled the airflow cells above 16. Then I raised CORRCL Airflow % and no stumble though it still had surge at cruise. Weird that after these 2 changes that now my MAP only goes to 70-75kPa when slightly coming off idle vs the 90 like before but good thing is no stumble. I kinda can make sense of this in my head but can't explain it haha so I'll just shut up on that one. I also set all BLM vs MAP boundaries back to zero due to odd cells while driving so I'm guessing that tunerpro had done this for a reason when I set SD and I should not have added these back in.
So I started playing with Ind Fuel Trim at 0% and >0% TPS with a infrared thermo gauge. I've had them all set to 1.000 and It took many test over a 2 day period to get them all within 15 degrees at idle. My very first readings my lowiest was 245 and highest 475. After each change I would drive the car for 20 min then let it idle for approx 5 min before taking temps. I was using 350/375 degrees as my baseline and all are great except cyl 3 is still around 450 at 1.000. I played with this cyl by it self for a full afternoon. I slowly added fuel from 1.000 it would raise temp up to 610 at highest, I started back at 1.000 slowly removing fuel and it got to 650 at it highest temp. I have swapped injector banks and no change with cyl 3 so I'm just living with it at 450.
I finally got the surge at cruise completely smooth at cruise by fine tuning ind trim at >0% TPS. Same way as before except had a friend hold rpms at 2k. I have all of these +/- 15 degrees though cyl 3 still higher than the others and I'm hoping it isn't something internal. It drives so much better from off idle to cruise like it was before all this and hope it stays this way. I wish I could get PE AFR trims correct but I need wide band O2 to safely adjust this right?
Still have an occasional hiccup at 4000/4300 rpm with nothing odd showing in log that I can see. I'm thinking that cyl 3 maybe the culprit because fuel regulator, filters, intake gasket, opti, plugs and wires are new. Really nearly everything except coil and injectors are new. I'll play ith with this issue and will start another thread if I can't get this resolved. So far all is well but haven't driven it in a few days because of the rain. Thanks!