hesitation/knocking problem

[SHIFTrl240]

im having difficulty trying to figure out what direction to take my repairs in... i have a 91 240 that had a 93 motor professionally swapped in 3 yrs ago (70k on motor) ive had no problems at all until now. i have a safc2 in the car because i was planning on turboing the motor over winter, but there are no mods to the car currently except for an exhaust and removed AIV.

before the problems occurred, the safc2 would read about 30 knock on idle, and it ran perfect without a flaw. im not sure when the symptoms started, it seemed like out of the blue because i dont have the safc mounted, i kept it in the glovebox. at one point i noticed that the car would studder or hesitate in the low rpm range (1.5k-3k) when applying moderate to heavy throttle. after 3k or so it would free up and become normal again. i also noticed on the safc that it would be knocking almost 80-120 at idle, and 6-15 from idle to 3k or so. and this only happened when it was cold started, and it would continue until the car was shut off for at least 20 mins after it had warmed up, then it would usually go away.

i changed the spark plugs and wires to see if that had anything to do with it, but alas i am here asking so that didnt work. the day i did put the plugs in though, i went on a 25 minute spirited drive to see if i could sense any hesitation at all but nothing. this was after i had already driven to the parts store and then had it off for 20 mins or so putting the plugs and wires on.

i appreciate any help i can get and i'll try to clear up this post if i can... its pretty long heh.

thanks