Yes the 99 will fit and it will have a better trail riding powerband. All the CR250 cylinder from 1992 to 2001 have the same overall length, the powervalves and studs fit the same way too. The only thing to remember is to match the pistons and heads. The 1992 to 1996 have domed pistons, and heads with angled spark plugs and the 1997 and later have flat top pistons with a centered spark plug.
Honda cast the insides of the cylinders different for various powerbands. Heres a quick run down on the models.
1992 The biggest ports ever! Problems with reliability though with quick piston wear and cylinder skirt breakage. For DTX and karting, the 92 is the best.
1993-95 The intake port is smaller to reduce piston wear but the exhaust was still rather large.
1996 The perfect off-road porting, good reliability too.
1997-98 A screamer with the sub exhausts raised and widened, low to mid range was a problem.
rebounded a bit too far by detuning the cylinder and shrouding the Boyesen ports and retarding the porting.
rebounds again this time advacing the timing so only RC could handle it. However this cylinder has great structural integrity with massive skirting.
Good thing Honda
lost the plans for the 1996 cylinder or I'd be out of business :whiner: