Quick points:
a) With modern computers and Windows 2000 or XP, you should not likely have to wipe and/or reinstall windows.
b) MANY eMachines use non-ATX compliant boards. Often they are micro-ATX (mid- to small-tower cases) but do not have their screw holes in standard spots, and often the cases do not either. If you are replacing the board, be prepared to get a new case. Realistically, it's a good step in the right direction to do so anyways, and slowly move away from anything even remotely proprietary.
Oh, and $300 for a motherboard? No fscking way!!! Maybe for an advanced multi-processor board. Not for an eMachine!
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