What do you mean by bigger engines into smaller frames? how big an engine and how small a frame?
here is a site taking about the conversion process for putting a kawasaki h1 500cc engine in an s-series frame (250-350-400). This may not seem like that much of a difference until you realize that the 750 motor shares the same mounts and dimensions. the 500 motor makes more hp than the 400 but because of the frame design was heavier and therfore only as fast as a 400, I have a friend with a h1/s3 conversion and that bike screams:
http://kawtriple.com/mraxl/khconv/400to500.htm
As for hondas it has long been a street racer's trick to get the cb650 SOHC engine and put it in an early cb500/550 frame. The early cb500s are lighter and the cb500 shares the same motor mounts with the cb650 so it is a bolt in.
As for more modern machinery, the fzr400 was imported into this country in 1988 through 1990. They are all alumnium and with lightening tricks can be brought down to under 350 lbs. The fzr600 is almost the same bike and an fzr600 motor bolts in directly to the fzr400 frame. The yzf600 motor and R6 motors fit with some minor modifications. Basically a 120 hp 328 lbs bike when you are finished. the fzr400 makes a great track day bike for a lot of people.
The cb350f four is a hideous lump of slow honda, can barely get out of it's own way, but a hot rod 400F motor fits right in. I have heard of people getting early 500 motors in there too but have yet to see one in person and don't know what is involved. the 400 four motor is a little barn burner.
The popular swaps with kz400s is to find a 440ltd cruzier style bike. Makes almost half as much more hp than the standard 400 and the mounts are the same.
As for road frames that aren't chopper, you can get a manx frame brand new but be prepared to pony up $4K. A t500 motor will fit in the manx frame since suzuki designed the tr500's frame by modifying an original manx frame. I'm trying to convince rosko to help me make some new cafe racer frames but he won't do it without a set up shop (right now anyway). I want to make slimline frames that take all the norton cafe racer bodywork but cb750/t500/h1-2/cb450/rd350 engines.