PCM Diagnostics & Tuning - PLEASE HELP! After LT Problems!

OK sorry for this being so long but I feel it necessary. 3 weeks ago I did Pacesetter LT's(ceramic coated), removed cats, mandrel 2.5" all around,Magnaflow dual in/dual out single stainless muffler,and LT1 fans. I had a number of exhaust leaks but fixed them all and even put Nitrogen through the system to make sure. The next day I started to get a terribly rough idle-it would go to 3k and back down and repeat untill it ran for about 5 minutes then it would start to load up. When scanning I wasnt getting consistent o2 readings so I replaced both front 02's(obviously the rears are gone and turned off) and they were both totally clogged so it was needed. Well since I got the new o2's(stock ones) it has gotten worse. It feels like when your driving with 7 spark plugs except worse-it bogs and loads up and sounds like I have a flat tire! But I can drop it in 2nd(automatic) and get it in higher rpms for a few seconds and it clears up. I can but it back in drive and most of the time it clears it up and drives fine. Then the next time I crank it up sometimes it will be better sometime it wont. Each morning though this is the case. Through this whole ordeal I have been tuning hoping I can fix it. I have tried in speed desnsity and MAF. At times we would flash it and it would be fine then start back up sometimes in minutes other times hours. We thought I may of had a corrupt file but I put my the tune in I had before the headers(that I had no issues with before) and it didnt help. Ive read about you F-bod guys having issues with your o2's heating up after LT's and I dont know if these sound like problems from that. I have a stock MAF but it is descreened(for over year now). COuld this be a factor? The only code Im getting now is a P0200(injector circuit malfunction). Please help Im running out of ideas! My mods in the sig a current! Obviously I had to adjust my tune after the exhasut leaks and after the o2 fix but now they are fine except when it starts to load up/surge. We thought for a second that I was running out of injector but that doesnt seem to be the case.

Thanks for the help! lol! Can someone tell me this- I just put new stock 02's in and their readings are consistent with one another-each morning my truck passes the 02 test and 02 heater test. If my 02's werent getting heated properly since being relocated with the LT's but are plenty hot enough for stock manifolds would I be getting any of the o2 DTCs? Im wondering if the pcm sees that the 02's are working fine and the heaters are working fine so IM not getting a DTC. Untill a few days ago I was getting the p0200 and would clear it and it would come right back but now I havent gotten it in 2days. What I get now is when it starts to load up the SES light just blinks. Why is this?