I have a 99 civic it has a Y7 block and a Y8 head. When I first put the engine in it ran fine for a couple of weeks. It then started to have a very bad hesitation. When I first start the car up it will run fine for a couple mins then it starts acting up. If I stop at a stop sign or a red light the rpms will drop almost down to zero. Then when I hit the gas the light will be turning yellow by the time I get through the intersection. If I'm sitting on a hill it's even worse. The rpms will climb to about 4-4.5k before shifting from 1st to 2nd and again when shifting to 3rd(It's an auto). Once it gets moving above 20mphs it will start to do ok it struggles to get up to speed, but as soon as I take my foot off the gas it starts acting up again and becomes more sluggish. I replaced the fuel filter a couple days after it started doing this, thinking it might be clogged. It was clogged up a little, but it still does it with the new filter on. I put new plugs in after I dropped the engine in. What could be causing this problem???