1.you shouldnt have problems doing a quick format, but I would full format it just in case
2.There shouldnt be problems(im assuming you will have both hds connected so the transfer will be directly between them) even if the transfer isn't direct and you have to copy everything to your pc drive first you shouldnt have a problem.)
3.this one is a bit trickier(but not too much), if winhiip cant "see" the codebreaker info, you could try to access your hd from ulaunch and copy your codebreaker info to a USB.
Do you have a partition specially made for saving your codebreaker data?
V7 ps2, flip top, 2x 8MB sony memcards, FMCB 1.8b, ESR r9b, Cogswap, Hdloader0.8c, 250 gig Western Digital, poorly modded(but functional) network adapter