I would start with spark plugs, with higher compression from the turbo, the spark can misfire. Old spark plugs with a too large gap will be a common issue. Other problems are the coils if you believe it to be a misfire. This analysis is typical if it feels like it jerks around as the misfire is intermittent. In the case of fuel starvation from a clogged fuel filter, it may not be as jerky. In my opinion, I have never seen a fuel filter replacement solve this type of problem. With turbos, ignition misfire is a common culprit.
Almost everything is new including fuel filter, cps, fuel pump. I also tried a back up di.
It seems to be back firing and missing unless I baby it and it takes awhile to start up. Its throwing a code for rear o2 but I don't think that's the problem though I will get to it.
I think what I'm going to do is run a bunch of fuel system cleaner and injector cleaner in case of a clog causing fuel starvation. And checking out those plugs
^ I'd just use whatever gas is cheapest and run a bottle of Techron through every six months. It's a much more concentrated cleaning. There's no difference between cheap no-brand gas and expensive brand gas except for the additive package.
I'd try and figure out the issue 1st before reflashing the ECM. Could it be an excessively worn timing chain? Also might be worth the time to check for bad wiring or failing vacuum hoses to something like the MAP sensor. I'd look at the DIC connector and wires, the CPS wires especially where it connects to the sensor. Maybe something in the fuel system is failing like an injector, etc. Hard to guess without the car in front of me.