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Hi I have a 2002 mercury Cougar 2L with 105,000. I just changed the clutch and slave cylinder last November 2016. Last weekend I changed the front brakes and rotors as a pad blew up and destroyed one of the rotors. I test drove it and everything worked fine. About two days later I started having shifting issues. From a dead stop it shifts fine from 1st through 4th gear but when I go to downshift it wont it acts like the clutch doesn't disengage. I have to come to a dead stop to shift into 1st or second. Also, starting from a dead stop I can push in the clutch and put it in first gear and it seems like its fine. Let the clutch out and start to go and then push the clutch in and give it a little gas I can feel the clutch trying to grab (so i am thinking the clutch isn't completely disengaging). As the slave and the brakes share a fluid reservoir i thought maybe somehow some air got in the slave cylinder line. I purged the line but it did not fix the problem. When purging it seemed like there was good fluid pressure coming from the purge line. I can only think when i changed the brakes something happened when i compressed the brake cylinders. I did it like any other brake job i have done by opening the reservoir filler cap when compressing the brake cylinders to replace the pads. Being a new clutch and slave cylinder I cant imagine that the slave went bad and coincidentally right after changing the breaks. Could something have been damaged in the master cylinder?

Need some help this one has me stumped.
 

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Perhaps some debris from the failed brakes has somehow found its way into the shared fluid reservoir (from your hands from the caliper pistons or brake lines) and then into the clutch slave cylinder. I'd try dismantling and cleaning the clutch slave cylinder and removing and flushing the clutch fluid line at the same time
 

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There is also the good possibility that that the brake job has nothing to do with the clutch fault what so ever and giving you a bum steer .Check clutch master cyl at pedal for any sign of fluid leakage .


P.s
Another thought .Check gear linkage / shift cable for wear .Wont help if worn .
 
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