On my 5-speed 240 DL (1989), 5th gear has a loud noise. It doesn't really sound like a mechanically-negative noise, like "marbles" in the gears, but just a loud, mechanical whine/noise that's similar to a race car I guess? Probably not though.

Less than 4,000 miles ago, a new clutch [kit] and new rear main seal were installed, I'm unsure if the previous owner had the shop refill manual transmission fluid. Should I try this first, and if that doesn't fix it, what will? I hope a transmission rebuild is not required. Even buying a used M47 will be expensive as they are seldom to find...

EDIT: I have a rubber shift boot, the accordion-style. So it doesn't insulate the sound very well, but if the problem is not mechanical and only cosmetic/audible then I don't mind.

 

Did it start all of a sudden or was it a progression?
That 5th is prone to this, basically the small bearing wears and, well, needs to be replaced, which is not cheap as any time you have to crack a tranny, it gets involved.
Assure that the fluid is up, change it with a little heavier weight all synthetic but chances are you'll need tranny work. You are right, the M47 are hard to get good used--they are prone to just that type of failure.
On the other hand, it will probably last awhile with the noise getting worse before you lose the 5th.

 

Here is the noise its making.

https://vimeo.com/80240031

Is this normal or should I still consider transmission fluid and/or transmission rebuild?

 

if you don't know when the tranny gear oil was last changed, its probably a really good idea to change it. the condition of the old oil will say a lot of about the internal condition of the transmission, how much metal particle is in it, etc. if chunks of metal fall out, well, then you'll be rebuilding it sooner rather than later.