Toyota Celica Timing Problems?

[ToyotaFanMan]

I have a 1991 Toyota Celica GT, which just recently aquired a brand new engine with under 50,000 miles on it. Complete engine replacement. Everything is working wonderfully except for a problem that I had once with the old engine (they are both the 2.2li 5fse efi engines)

If I am parked and out of gear and at a normal idle rev say...500-600 rpms and suddenly floor the accelerator the engine briefly stutters (and makes a kind of "ting-ting" noise that matches with the stuttering). The same is true if I am in any gear around 2000rpms and try to give it gas- like to go up a hill or accelerate. Last time this happened the car eventually "slipped" and I lost 80% of the power and it "stutter stepped" continuously until I took it to a mechanic who told me that my spark plug wires were burned up.

He replaced them and the car gained a little power back...it actually had the continous power (didn't feel like I was losing power) just not near the raw horsepower it had and it still stuttered constantly. After about a month of driving it that way- it fixed itself one day, I shifted to third to pass (which was a long ordeal with the power loss and stutter) and the car just kicked in and took off like normal. Now it is a year later and it is starting to do it again. I know it can't be the clutch because I had a new clutch assembly put in with the new engine. Is it a timing problem? or perhaps a fuel filter? Any help would be wonderful!