Hi I had a mugen 4.9 FD in my 1998 integra type r for a 1 year now. The 5th gear is a stock LS 5th gear. I never heard it grinding in 5th gear before for a year. But I haven't been high reving it for a year. I just start working at a job where I use the freeway more often and when I rev to 4k or higher and shift to 5th gear it grinds. Anything lower and it doesn't grind.
Why would it grind like that when I shift to 5th gear at a higher RPS?

 

Try changing the Tranny oil first if it still grinds then i think the syncro on your 5th gear needs replacement

 

I had a very similar problem with my ITR. The only gear that had a grind was the high RPM shift from 4th to 5th. I flushed the tranny with Honda MTF but it stayed pretty much the same so I ended up replacing the 5/R sleeve set and a new ITR 5th gear and all is good.

 

Changing fluid can mask the problem, and even eliminate it for the most part, but it's a band aid, the real problem is the 5/r synchro set. Unless it's really bad the gear itself is likely still fine.