Mitsubishi Repair: 96 Eclipse, RS manual, clutch alignment tool, clutch fluid

Question
Recently I had the clutch replaced in my car because it wore out and after it was replaced I noticed that shifting was a problem.  When I would shift from 1st to 2nd gear it would now grind and the same thing would happen when I shifted from 2nd to 3rd gear but not as bad.  It happens both on the up and downshifting of the vehicle.  All the rest of the shifting is fine but the overall acceleration seems a bit more sluggish than before like it is being restricted somehow.  I have since benched it because I am not sure what to do.  I took it back to the mechanic and he tried replacing the slave cylinder thinking that might be the problem and it didn't resolve the problem.  He then suggested that I replace the master cylinder but beyond that he wasn't sure.  So I then took it to a transmission garage and the mechanic was saying that it sounded like something was internally wrong with the transmission.  So is it possible that when the new clutch was put in something was done wrong to cause these problems to occur.  Or does it seem that when the old clutch went bad it caused the transmission to go bad as well and now that there is a new clutch it is causing conflict with the old tranny.  I am at my end with it right now so any feedback would be great.  Thanks  

Answer
Bryant,
Replacing the slave cylinder and replacing (or rebuilding) the master cylinder are good first steps.  The clutch fluid should be bled of air completely.  The fluid level should be checked to be sure it's not leaking.

Else, confirm with the mechanic that performed the clutch replacement if he did the following:
- Drained and refilled the transmission fluid with the proper fluid as recommended by the manufacturer
- Replaced the throw-out bearing
- Used a clutch alignment tool when installing the clutch
- Inspected the release fork and pivot ball for damage or excessive wear
- Properly torqued all the tranny housing bolts
- Resurfaced the flywheel to factory spec, or within tolerance per factory spec.

Failure for your mechanic to follow all of those procedures can lead to hard shifts and grinding problems.  Older Eclipse are known for clunky shifting, but if you didn't have these problems before having the clutch changed, odds are your transmission is fine.  Confirm with your mechanic to be sure they performed those procedures, and maybe your mechanic will get more ideas as to what they did or didn't do.
Good luck!