have you had a tune since the Long tubes? how long have they been on?
about 3 months after putting my long tubes on, my car started running like ****. it idled like i had a large set of cams in it, and if i held it at 1200-1500 in any gear, it would start bucking and cutting out really bad. replaced new maf, new camshaft position sensor, new plugs... pretty much everything i knew that could cause it, and it still didnt fix it.
took it to my tuner, and he ran it on the dyno for a bit and datalogged it when it started cutting out, and ended up being my long tubes causing it. When you install long tubes, you extend the O2 sensors so far down, that at lower rpms the exhaust was actually cooling off before it allowed the sensors to get a good read, and was the computer was trying to compensate for the weird readings it got. He tuned it and fixed all of it
sorry for the long book, but just giving you some ideas?