I just took in a R150f for repair with about the same mileage. It was noisy in neutral with clutch out and first popped out occasionally. Took it to a local shop and they told me I was about to lose 5th gear also because of a spline issue. However, they said on my version (1998 tacoma) Toyota inexplicably partially splined 5th gear so some splines were broken (it looks like your 5th is partially splined).
He told me he had a shaft/gear with all splines from another trans so he used that for the rebuild. Also he told me 2nd gear synchro worn and this was probably due to backplate? wear which allows the shaft to move (again assuming I heard correctly).
I'm in it for $1200, had I known I would have considered a Marlin rebuild even though I would have to wait 4 weeks.
I bought my truck new, have done some low speed towing around town but don't think I have ever hit 5th gear while towing.
When I first bought my truck it had an annoying 5th gear whine and I tried to get a warranty service on it but Toyota denied it. I researched some and I saw a website (Toyota dealer service) that stated there was a design defect on 5th gear - something to do with a bearing being out of alignment. I even e-mailed him and he confirmed but then he quickly took down that notice on the web page.
I posted on a board about this issue and several other people with 98's e-mailed me that also had the whine. The whine went away after about 50k miles. Don't know if this might be the cause of 5th failure or it's just because of partial splining.
You obviously know a lot about transmissions but perhaps get a non 98 R150F from a junkyard or fully splined 5th + shaft.
P.S. I thought about this some more - suppose the gear shaft is not aligned precisely in relation to the driven gear (due to bearing location design defect). Then might the gear load the splines unevenly putting all pressure on one end of the splines, thus slowly chipping away at the splines? I noticed that in a earlier post here someone bought a new replacement 5th gear which is partially splined thus implying that all post 1998 R150's have the partially splined 5th. And if they had the same issue as the 98's we would probably have heard more about this. In any case a rebuilt 98 trans should go another 200k miles so I'm not too concerned.