I can tell ya, fixing the air cooled 200cc yamaha blaster engine is WAYYYYYYYY easier than fabbing up everything needed for an engine swap... especially a 4 cylinder engine swap. Most of the race bikes (CBR, YZF, GSXR) use downdraft carburetors (or downdraft throttle bodies for the later models with fuel injection) and ram air pressurized airboxes. The airbox can be modified so that it's not ram-air (you'll lose like 4 hp off of the top end) but getting around the downdraft carburetors is TOUGH. They go right where the bottom of the fuel tank is...
Unless you have plans of drag racing this quad, there's no need for anything more than a decent running blaster engine. They put out PLENTY of power for playing around, trail riding, or even (in class) drag racing...
If you're concerned about your machining skills, take the cylinder to a local machine shop and have then power hone it for you. They'll charge a few bucks and you'll be back up and ready to go in no time.
Order a set of cylinder rings, move your carburetor needle 1 clip down and begin the break-in procedure.
You'll fall in love with 2 stroke power before you know it.