Everyone, oh Everyone!
I'm not sure Everyone will reply to your post, but I will
Yes, DK64 slows down for me in various places. I even get a cool Matrix-like effect here and there.
You should use the handy 'search forum' feature at the bottom of the main pj64 forum screen, if you haven't found it. There are hundreds of posts dealing with DK64 problems. I have not played it much, but you will definately need to read those posts, if you haven't already. I don't think it is possible to finish the game without reading them.