Guys,
I am suggesting that you consider checking your work on the hydraulics. There can be lots of reasons for shifting problems, but if you want to rule out the hydraulic system as the culprit, a simple test can confirm the status of the system.
With any master cylinder and slave or caliper combination air is the enemy. Trapped air compresses and we do not get the same amount of travel at the slave cylinder as designed and what the clutch needs to do its job, release the disc.
Suggestion:
Remove the slave cylinder from the housing leaving it hooked up to the line. Get a steering wheel puller or damper puller that has a flat bar, not a jaw type. Bolt it to the slave after you carefully remove the piston and boot assembly. Use the puller screw to block the slave piston, use care.
Now, with the system blocked, push on the pedal with your hand, do not do a pressure test at this time.
Air will show up as a spongy or soft pedal.
The master cylinder pushrod will only travel about 1/8" before lock up with the fluid, any longer than that and its time to look for air or worn pedal cluster components.
Bleeding.
This bleeding is not like the traditional pump pedal, hold, open bleed screw and waste fluid. I suggest that you use the slave cylinder as a pump to flush all of the fluid in the slave up and out into the master, this will push air bubbles out, let is expand back to normal length, repeat several times. Possibly have someone watch for bubbles to appear in reservoir.
Check your work by screwing the puller screw back in and test for shaft travel to pressure point.
You can also remove the entire system, take it to a bench, block the slave, use the pushrod and push on it. If it moves more than 1/8" time to bleed. Orient the entire system so you do not have any air traps, let the air go up and out the top. Set up a slave pushback arrangement, I use a 3/8" extension and push the slave down on to it, always with the air able to flow up. It helps to tap the slave and line with a tool to dislodge air bubbles and get them flowing up and out. With the slave blockes, test again, you can also short stroke the master pushrod to trigger the check valve in the master to burp out air.
I'm in the process of doing some hydraulic training videos right now, still feeling the unpleasant tingle of DOT 3 right now on my hands.
Bleed screws sometimes just waste DOT 3, you can pump it out using the already installed slave cylinder and there are other methods, like vacuum on top of the fluid reservoir, another good tool to keep in mind.
I would not like to see mechanical systems make a comeback, hydraulic clutch release systems have a lot going for them.
Good luck.