the gen5/6 502 uses a cam thrust plate and no bearing against it. so normally you dont need to set thrust, especially since they use roller lifters. you dont need to remove the intake to measure cam thrust movement, just loosen all the rocker arms. then remove the timing cover. not real easy to do without dropping the oil pan some, but can be done. however, it sounds like you have a timing cover that has a removable access to the cam since your useing a water pump drive system. this is driven off the cam correct? you may have a system that was designed for a mark 4 BBC. the gen6 roller cams are differant at the timing gear end. machined smaller with closer mounting bolt holes. but, the over all length should be the same. i realize i havnt givin much info on how to fix your problem, but some reasons why you may be having the problem to begin with. i would suggest posting this also on the V-drive forums ( if you havnt allready) since it is most common to use a cam driven water pump with that set up.