Irvin is correct, it's all about the mounting. I've restored more than a few shortened/deformed frames, mostly Head frames, back to original by simply 'stretching' the frame by the exact measurement. Btw I use a 6-pointer and I'm not sure if it'd work with a 2-pointer. So for example if it's 2mm short, just stretch the frame by 2mm with the 12 o'clock mount the next time you string it and it will come out perfect, trust me. Also it depends on your machine. On certain 6-pointers, there is more flex than usual and the frame needs to be stretched a few mm's for every stringjob to ensure it comes out the same.
Regarding the tension for mains and crosses, it's not really an issue if the difference is not too big. Even with Head frames I've done the crosses 3-4 lbs lower than the mains in a full-bed setup before (same string both mains and crosses) and with the correct mounting it always comes out perfect. I'd imagine the frame would start to deform if the difference is like 8 lbs in a full-bed setup.
But of course, if it's a poly/multi hybrid it'd most likely be fine to string the multi 8 lbs higher than the poly.