XTZ660 regulator problem

Just before christmas, I was given (yes, there are nice people out there) a non running 1993 XTZ660 3YF and was told that all I needed to get it running was a cdi unit, regulator/rectifier and a coil (and a lot of cleaning). I purchased these items on e-bay as well as a Yamaha service manual. My query is the new regulator/rectifier, which is a small rectangular ish black box (the same as shown in the manual) is totally different to the one attached to the bike, which is a large thing with fins. Is it just the case of swapping the two items over or do I just use the original one (I was told the new cdi and reg/rec are designed to work together). Not being electrically minded and also being very short of cash, I need some advice as to what to do, preferably as cheap as poss......... Ta