98 SC2 Manual 5spd won't shift

Thanks for the help on my other post. I ended up having the transmission in stalled by an ASE certified mechanic. The transmission has 7000 miles on it, the clutch has 5000. The car has 90000. Now it is very very difficult to get into 3rd and 4th most of the time, sometimes into 1st or 2nd. Pumping the clutch pedal doesn't help. I have read that you can adjust the shifter cables, but my manual doesn't tell how and I can't find information on that on here. The mechanic says he thinks it's the clutch hydraulics and to replace the entire setup, does that sound like a possible fix? He said the fluid is black and rubber is rotting in it, but it looks pretty clean to me, except some junk is floating in it. Money is tight, any suggestions greatly appreciated! Thanks in advance.