02-08 "should" interchange for the most part , the one who could tell you for sure is Ken , the owner of the site , but he was in a accident recently , and is pretty banged up , so he has not been on here much because of that .... I would say to confirm with a Honda Dealer , but they won't really know , as they would just go by part # and if #'s are different for different years , they would not know what to tell you other than part #'s are different , but that does not mean they won't fit , it is usually just a updated thing , like compression ratio or something that could make a part # different , even though it would still directly fit ....
What you might try to do to confirm , is to call a engine builder like Pro Circuit or something , and ask what specific years top/bottom ends will directly swap as I have not tried mixing years too much , but I know cams(with towers) and heads and the crank will all interchange , flywheels are different , but only in weight , but will still bolt up ......................As the only thing I can come up with is that the chain is being held from relaxing all the way by something , which is why I asked about the tensioner , but 02-08 chain should fit any 02-08 engine configuration , so I would "assume" that any year swap would give the same result .... as I don't believe they changed cylinder height or anything like that thru those years , and I believe all the heads of those years swap out , and 02-04 are pretty much the same bike with the exception of internal suspension items and subframe (but they will still swap if you swap muffler system as well due to mounting difference , but I ran a 03 swingarm ,linkage and airbox along with a 05 carb on my 02 with no issues ......not sure what else it could be , that is why I thought tensioner or tensioner guides holding it from having that extra length you are seemingly missing ...
