Metamorphosis

Hi. So I've bought my Civic 7th gen. 2001 (D14Z6) few months back. I did had some problems with really powerful engine braking when comming to a stop, revs dropping to almost 0 on changing gears and jerking on low revs (1000-1500, no throttle).
I've been playing with TPS (through OBD it showed TPS at 5%) and idle screw for some bit, back and fourth, cleaned EGR, throttle body and IAC valve. Finally I've changed it with a used throttle body. TPS is showing now 9,4%, engine load dropped from like 35 to about 25% and it does sound a lot better.
But I still have a few problems with it.
1. When I press or depress throttle it jerks once, it's better on higher gear but still can feel it.
2. Taking off is really unpleasant. Can't really do that from clutch only (did that just to check, clutch by itself is ok, no problems at all when moving). I have to rev it to about 2000 at least and when revs drop I can feel how the car rattles. When coming to a stop and it drops below ~1700 engine braking becomes even stronger.
3. Maybe I didn't reset the ECU properly but when comes to a stop revs hang on about 1600 for a few seconds. Sometimes even fluctuate ~200 up and down.
I still have to do valve adjustment on it but is it possibly it comes from a vaccume leak somewhere?
I can check some OBD readings but I'm not sure which one should and what range they supposed to be at. Any ideas? I would give this car an extra 5-10 years of life.