My clutch seems to have two issues. First, it doesn't seem to disengage all the way, since its difficult to get into gear when driving, but it does go in. The other thing is, when I let the pedal out, its almost like it sticks, then all of a sudden releases. You can actually hear a bit of a metallic thump each time about halfway through the pedal travel as it grabs. There is also a ticking noise while moving the pedal in and out, but not when the pedal is still.
I had the clutch and clutch fork replaced about 10k miles ago and I rebuilt and bled the master cylinder too.

Wouldn't be surprised if your clutch was going again. Mine grenaded at around 12000 miles, came out in 3 pieces, the thread with pics is up here. It was doing some similar things.

Did you replace the pilot bearing? They are often overlooked, and can make your clutch drag like you described. They do a lot of work for such a tiny bearing...

Check the bracket under the dash and the firewall where the clutch MC bolts to see if they are cracking. Known problem on Toyotas.

Yup, sounds like someting in the pedal. Cracked bracket, or the clevis pin that holds the pedal to the master cylinder is loose.

I did check the pedal and the linkage when I rebuilt the master, but I'll check again. I know for a fact that the shop didn't replace the bearing (is the pilot also called the throwout bearing sometimes?). I just assumed that it was done when a new clutch was put in so I didn't ask until after (my own fault). Guess there's no way to know for sure without having it all taken apart again huh?

Pilot and throw-out are not the same. Both bearings should always be replaced when the clutch is done, especially the throw-out.
Before going to the expense of the clutch itself, replace the MC with a new one (they are inexpensive). Most people don't rebuild those things anymore. A bad MC can also cause those symptoms.

What would be bad with the M/C besides all the guts which get replaced?

You may not have done a good job replacing the guts, and the little rubber piston thingees could be binding. This happened to me once.

Also check the clutch pedal pivot bolt and bushing. The clutch master can also make the pedal feel like it's "clicking".