Im converting a 1979 9.9hp johnson from a long shaft to a short shaft and want to know if anyone can tell me how to remove the copper water tube out of the power head after I have removed the lower unit.

There were two ways the tube was installed in the 9.9. One way was that the tube was flared on the powerhead side and the power head had to be removed and the tube dropped down thru a hole in the flange. The other was, the tube looked the same on both ends like a champher cut and was stuck into a grommet. That style was easy, just pull the tube, and out it comes. If you pull the tube out like that and it is flared,,,,,,then you get to pull the powerhead. Which is not that bad of an idea, cause inside is the shift rod. and I've seen the connecting pin almost rusted into.

Thanks Mike. Should I try to cut the tube off to the right length or replace it with 1 for a short shaft?

You will almost have to be a mechanical engineer to get the exact measurement that you need and you will be up inside the exhaust cavity to cut it......naw. Just get the short tube...