Low power when accelerating to pass or go up hill

I replaced the engine three and half years ago with one that had 155,000 on it. Every thing has run fine until about a week ago. I always let the car warm up for ten to fifteen minutes before I run it cold or hot weather. Once warm and ready to go I will drive for about twenty minutes and then I will have a problem. The problem is the when I have to accelerate fast to go up hill, to merge on the highway, or to pass another car there is a lag in the engine. The engine will rev up and I will be pushing 3500 to 4000 rpm's and I will then hear a clunking noise in the engine for a few seconds. I have noticed that the car shifts slow during this time causing the engines rpm's to rise. If I am driving at a constant pace everything works okay. It is only when I need quick acceleration that I am having this problem. Any thoughts of what to look for?