yo bro ,
i`ve been having clutch problems since i converted my engine 4G63 , and that was a year ago , i had shifting problem's just like you , i assume it was the gearbox , but then i had read up on troubleshooting hard to shift , i did some research , all the answers i found was , clutch clearance is not right , clutch installation without proper tools and alot of the answer i get is related to clutch .
so from my experience , before wasting alot of money , do touch up those simple simple stuff first , like your upper clutch cylinder pump which will cost about RM 30 , and then lower pump will be about RM 16 , then bleed the lines , and make sure the clutch adjustment at the clutch pedal & below the gearbox is been adjusted correctly .
here are some pictures what i did recently , when i did my clutch replacement , i change everything related with the clutch & gearbox . so that i wouldn't have headache in future .
1. Gearbox mounting
2. Driveshaft cover
3. Driveshaft oilseals
4. Upper & lower hydrulic piston pump
5. Exedy standard 4G63 clutch cover & clutch disk
my upper & lower hydrulic piston pump , which is in a bad condition , by looking at it , its been scrape unevenly , which makes the clutch lose pressure .
my clutch was uneven , so its not gripping fully and that relates in hard shifting gears . i`ve been using the clutch for 1 year and abuse it quite frequent , surprise it still can be used for maybe 20,000km more .
lower hydrulic pump , badly damage , replacement kit is RM 16 for the lower ones .
picture below , shows the clutch fork which you can adjust it by taking it out and twisting to your clearance liking .
if all this does not work , then you are just loosing like RM 100 bucks only , rather then changing the gearbox in the end your problem is still not solved , u`ll be wasting like 800 bucks just on the gearbox and 100 ++ for the workmanship .
so good luck man , all this info is based on my experience . i`ve solved my problems by doing all that , without changing the gearbox . :lol: