Is it hard to shift into gears even when the vehicle is off? There could be a lot of things, but let's do a checklist and start with the simple things:
Yes, you can easily inspect to see if the throwout bearing is riding on the clutch preasure plate fingers from the side of the bellhousing. Make sure the vehicle is off. You can look on the side opening (if it's still the orginal transmission, the inspection port will be on your passengers side) it looks like a little rectular window..... Using a cell phone with a camera to get in there will be the easiest to see eveything. Or you can just remove the bottom inspection cover of the bellhousing and look as well.
Also, not sure, but was your entire clutch, flywheel, pressure plate replaced? I'm just thinking, but if it did, maybe the throwout bearing got put on backwards. You can check to see at the same time as the step mentioned above.
2nd would be to make sure the fork is adjusted correctly at the slave cylinder. If I remember correctly, there should be 3mm-4mm of play. Then you check the pedal height and pedal freeplay at the master cylinder. That can be adjusted inside the drivers side foot area of your Fj40. There's several forum posts on ih8mud that go through this. A bit confusing at first, but once you get down there and see how it works, you'll understand it.
3rd would be seeing if your master or slave is going bad. But they tend to last a really long time. The original from my Fj40 bit the dust after 40+ years, so I had to replace it at that time. But even then it was still drivable and I didn't have difficulty shifting, it was just leaking fluid. I Doubt yours is bad since you just replaced it.
Next thing I can think of is that maybe the clutch disk got put in backwards. I think you're able to see it through the bottom, but it's really difficult to distinguish, but still possible.
if you're able to shift when the vehicle is off with no issues from 1st-3rd gear (assuming you have a 3 speed) but not when driving, at that point maybe one of your syncro rings is completely worn out and would require for you to replace that part inside your transmission. Or you can just double clutch everytime you shift.
So easiest is just to inspect the throwout bearing and adjust your pedal free play and slave cylinder. Let us know what you find out after that :]