The botom end may need rebuilt, but that's not the cause of the low compression unless the rod is majorly bent (unlikely). The likely causes for the low compression are
1) engine not broken in yet = rings not seated = low compression
2) Ring not gapped/installed correctly
3) piston clearance way too big = wrong piston installed
4) cylinder damaged/worn out/out of round
5) wrong or too many head or base gaskets used
6) powervalve stuck open - not installed correctly
7) major head gasket leak or loose spark plug.
On the bottom end thing....
When the top end was off, did you note any verticle play in the con rod big end bearing? Any play in the main bearings?