I was taking off the shifter on my 1989 GTU to install a short shifter on it. When I got the shifter off the fluid on the bottom was grey. I was wondering if I can flush it so I can add new gear oil in it?

 

Suck the old oil out with a hand pump. If you have one of those vacuum brake bleeders (e.g., Mity-vac), that would be perfect, or any cheap plastic fluid transfer pump would do the job.

 

I agree with the above. I use a fluid sucker or a Mityvac to suck the gear oil out and then I wipe out what I am able to with a rag and then refill the shifter well with the appropriate amount of gear oil.

 

Before you get too carried away, a small note. The gray color is most likely from the molybdenum grease used when assembling or reassembling the transmission. It goes between the input and output shafts so that there isn't a dry first start on that intermediate bearing. Once oil gets to circulating, it washes around that small bit of grease. On these older transmissions, and other sliding parts, a little moly helps out a little bit in filling some of the microscopic pits in bearing surfaces. You might be alright to leave it be, but that's up to you