if you read a low compression in a cylinder this is not to bad to fix.you just need to do a topend rebuild and this would consist of buying oversize pistons and finding a good machine shop to bore them out and fit the new pistons.the cost of this is around 400.00 and you would have a brand new top end.
sometimes you can just rering the top end or just buy new std pistons i have never done this i allways bore to the next size and make it all new.
what gets expensive on these engines is when they throw a rod out the block i have fixed 2 engines that did this and each engine cost me around 1000.00 to fix.
i totally rebuilt the first one myself new crank,cases,pistons,cylinders and all the machine work around 1000.00 total
the other engine i just bought a good used engine off ebay cost 900.00 still running fine though.
my 9 year old little girl loves these ski i could not sell them if i wanted to it would breake her heart.
1997 yamaha wave venture 1100 rebuild (part 1) - YouTube
crankshaft is here - Copy.MOV - YouTube
hope this helped you