Did you, after getting the install done... run a 4GB patch kit on SH4's .exe or barring that being used... use Large Address Aware... ???
Is odd, that you are having a CTD when running through the Rec Manual.
Either that, or instead... are you running into a CTD, with being in the Museum then not backing out of the game/sim, entirely before going for starting up a nav map trainer...
Seem to recall that going into the Museum then starting a training mission or just flat out, starting off on a career, after a visit to the museum... could cause that to occur.
1 last thing... when you nuke vaporized the previous install... did you also... remember, to nuke the games save folder for the initial install... & not, reusing it when you reinstalled SH4 then the mod set...
This can also cause a wealth (& not a good wealth, at that...
) of issues in & of itself, as well.
M. M.