2000 Honda Accord SE jerking consistently?

Im working on my 2000 Honda Accord SE 2.3L SOHC with an F23A1 engine
and BAKA transmission. The problem is a surge or jerk when accelerating
and decelerating at almost the same time in rpms every time. I just took
everything off down to the intake manifold gasket. I was doing this to replace
all gaskets, seals, and o-rings beause of oil leaking into my coolant reservoir.
the problem with the oil leaking into the coolant was fixed but now its got the
surge/jerk. Initially after me and my dad cleaned and replaced everything
from the intake manifold gasket job, everytime i went to accelerate even a
little bit, the car would shake, stutter, then stall if enough was pushed (and
little smoke would come out the steel mesh part just before the catalytic
converter on the exhuast pipe). dad said the car just needs enough time to
reset itself so i let the car idle for a long time and drove it on the little speed i
could around the neighborhood. it DIDNT change. p0505 popped up and it
said something about idle air control system malfunction. So i removed the
idle air control again and i looked all inside and it appeared to be ok clean(no
major carbon) and the spindle inside moved pretty smooth and freely, but i
still sprayed some throttle cleaner in it and some black came out. I put the
idle air control back on and everything down to it, started the car up and the
stuttering and stalling went away. Now there is still a jerk, when driving on D4
the first time it switches gears it jerks and this is consitantly at the 3250 rpm
area, when the car decelerates (using brakes or on its own) and gets to
around 700 rpms the car jerks again. every single time it will do this, but only
if it switches gear at 3,250. if i never go above 3250 or let it switch then it
doesnt do the jerk at 700 rpm's. it seems that when the 3250 jerk hits its a
boost forward and the 700 jerk is pulling back. some side things that might
help is when i depress the brakes it sounds like air under steering column
area. it hard shifts from park to reverse (with some small car shaking),
Neutral to reverse is hard, medium shift to d4, d3 to 2 is hard, 1 to 2 is hard,
every other shift is smooth. the car hits 2k rpms at 10mph and 3k about
20mph. The tranny fluid was brown and i did drain and refill. the problem
occured before the tranny fluid change and still exists after. The transmission
oil and the engine oil are both just below the max line and both appear clean
and newish. (drove around after tranny fluid change, mixed with some old in
tranny still). We had also removed and replaced the valve cover. Also, the
brake pedal didn't make the air noise under the steering column after the
intake plenum was removed only after the other side of the brake booster
hose was disconnected, it made a hiss (no clue why). Before the intake
manifold job there were no transmission switching problems or jerks.
Does anyone have any idea what this problem could be because of or where
i might start to check? then after i check that and its all good, where to next
to try to fix it?  
thank you for your time. sorry for the story book.