If fuel pressure, ign mod/coil pack, and ECM are good.....I would try removing the Powerlogger and see if the problem goes away. I have noticed on my car, if the PL is not firmly attached to the ECM, it will do weird shit like you described. I run a Scanmaster thru the PL as well and I can watch the Scanmaster display erroneous readings while driving on the highway even though the car is running fine...and then sometimes the car would just randomly start running like crap and then die. Double check you have a good connection from the PL to the ECM to include making sure you have the protective coating fully removed from the ECM contacts.
I seem to have "fixed" my problem by using long zipties to wrap the PL module to the ECM so there is no chance it will pull off the ECM. Especially when plugging in the USB cable into the PL. Yeah it sounds ghetto but it works for me LOL.