Are you finding sync problems during previews on the timeline? I've never had any problem with chroma effects but often find complex transition are not smooth. I'd suggest exporting only a small section including your chroma key and checking if the final product will be OK.
Another trick is checking track syncs with frame by frame preview using the cursor keys. The playback is not realtime, but you do see the rendering of every frame.
Can explain more what you mean 'chroma key is slow' and 'can't align video tracks exactly'.
Also what is your computer spec and the video format(s) and source(s) you are trying to align, are they from different sources or different frame rates?
Best way to work with chromakey is to split your movie in many parts, (scene) you apply chromakey to each part of your entire movie. When your work on part A computer recalculate only the part A of your work and make nothing for others parts. Avoid to use many video tracks because working with more than 5 to 7 video track slow the computer the CPU cannot calculate everything. Also close unused program using your program manager (Ctrl Alt Del). You need 16 GIG memory and a good top shape computer, longer the video more to time to wait.