1999 Isuzu Rodeo Question Car is having a hard time accelera

Here is a bit of history on the car. In the early part of July I was driving on the highway and instantly my car went from driving smoothly and quietly to driving like a nightmare. The fan clutch was roaring, the engine seemed to be working to hard AND my car began to have trouble accelerating in the lowers gears. Thinking it was a transmission problem that neither my fiance or I have any knowledge in fixing we took it to AAMCO transmission center. They found nothing to be wrong with the transmission after having given my car an internal scan and a transscan. So they asked if they can do engine diagnostics which was a series of 12 tests and cost me about $125 to run the tests. I gave them the go ahead. What they found was that my intake manifolds needed to be cleaned and my EGR valve needed to be replaced. When all was said and done I was charged $485. The car was running like a dream quiet, smoothly, and like I ahd remembered it running. Three short weeks later my car does the exact same thing while on the highway 154 miles from where I took my car in the first place. Not knowing what to do we took the car to a mechanic that my parents have been using for a while now and for some weird reason the man cleaned out my manifolds, replaced the fuel filter and cleared out the cars airflow system. WELL the man didn't drive the car and he said it was normal for it to be roaring like that, so we paid 202 dollars and left the place. We drove it back to San Antonio (154 miles) and took it to the initial mechanics. They checked it again and swore up and down it was my fan clutch. They wanted to charge us 300 so we took the car back and did it ourselves. WELL the fan doesn't roar at idle anymore BUT it is still slow to accelerate and it still revs at 2 to 4 thousand RPMs in low gears EXCEPT now once we hit a certain threshhold the car does this jerking motion and it clicks and it runs PERFECT it picks up speed like a dream. It's quiet it accelerates at regular RPMs with out hesitation. BUT we go through the same song and dance once the car is turned off. So my car now has the up to standard air flow, a new massive air flow sensor, fan clutch, fuel filter, and a new set of spark plugs. Some one suggested it could be the computer others say its the transmission. What do you all think?