94 Geo Prizm 1.8L LSi

[Tristiacon]

History... Bought car used off Craigslist and it ran great and awesome gas mileage but now we have some serious problems going on. It started puttering after we put in this tank full of 100% gasoline in the car. Bad, bad idea. It began to putter and misfire. Found a clogged pre-cat and since it's an older car the manifold converter (pre-cat) is no longer manufactured for our car, used or after market. So we decided to straight pipe it and bought a new manifold header and flex pipe to convert it from a CA emissions to just federal emissions. No exhaust leak now... With the misfire we fixed a cracked distributor cap (cap only) but left the rotor. Anyhow... Here's the issue we're having... It continues to putter and misfire... It's sounds like this (lol) putt..putt..putt..puttputtputt..putt..putt..putt. So now we're gonna change out to NGK spark plugs and wires, plus add a new rotor to the cap. But if it continues to misfire what could be the culprit? And what possibly could of this non-ethanol fuel have done to our fuel system line to cause another problem we have and that's now a serious case of loss of power upon exceleration, poor gas mileage and even increased oil usage. No blue or white/grey exhaust smoke coming out of the exhaust either. The motor is strong too, so if anyone has any ideas we would greatly appreciate it...
Thanks for any ideas.
Tristiacon in Oklahoma