I have just done a quick search online for a 50k 90 degree pot with D shaft and came
up with the following:
5 Pcs 50K Ohm 90 Degree 6 Terminals Dual Linear Rotary Potentiometer
from Amazon Amazon.co.uk
3pcs CF R161ON-B50K-20F-C 90 degree B50K single potentiometer / handle length 20MMF
How appropriate these suggestions are as replacements is debatable.
You sound like you know what you are doing so I assume you have ascertained the type
[log or linear] of the original.
I too possess an ancient saitek yoke. I have had it apart a couple of times over the years. But only to
clean and re-grease it and replace the dead LED’s in the clock. To my surprise the pots were [and remain] fine.
Perhaps some more research might yield some better candidate substitutes.
Have you tried speaking with Logitech [the now owners] to see if they will supply your needs?
If all the above falls short, what about trying to revive the original offending part with the judicious use of some proprietory switch cleaner. Or an overnight bath in isopropyl alcohol?
Maybe you can find a used yolk going for spares at a good price on ebay that you can cannibalise.
Sorry I cannot help you directly.
Let the forum know if you have any success.