Please help!

My Toyota:
Toyota 4Runner 1988 SR5 22RE W56B transmission with the original clutch, 33" tires, stock height in the front, rear 1" higher than the front after Zuk mod, 130000 miles on the clock.
It is our holiday vehicle, mild off road every summer, nothing hard, we don not tow any trailer with it.
Our Toyota runs 3000 miles per summer (mostly highway), stays in the garage the rest of the year.
I am the second owner, the first one did all the maintenance in a Toyota dealership, I have all records, it looks like he took care of the 4R, it is in excellent shape for its age, I do not know if the previous owner used to tow a trailer/loads with the truck.

Note 1:
I have been driving manual transmission cars/trucks for decades, I do not have experience with automatic transmissions, in case you wonder.

Problem:
The manual transmission does not shift smoothly.
There is some resistance (it grinds if I am not careful) when I shift from 1st to 2nd, and sometimes happens from 4th to 5th.
The clutch feels spongy.

Note 2:
I started to notice the problem a few hundred miles after installing the Zuk mod.

What I did until now:
I tried shifting with the rpm under 800 from 1st to 2nd, sometimes works.
I tried double clutch, sometimes works.
First I replaced the manual transmission oil with AmsOil synthetic Manual Transmission SAE 75W-90 API GL-4. After a while, same problems.
After that I found a small leak/drop in the master clutch cylinder. I replaced it, and the slave cylinder also from MC. After replacing the fluid with another DOT 3 and bleeding the system, same problems.
Later, I found out the gear stick seat was disintegrated. I replaced with MC heavy duty seat, and I also installed the MC heavy duty nylon shift lever bushing (socket). Same problems.


Please, help me to solve this issue.
Thank you.

 

Only other information i would want before making an educated guess? How old, condition, mileage, etc is on the actual clutch?

 

The truck is a 1988 4R, original clutch, 130000 miles on the clock, I don't know its condition.

 

Have you properly adjusted the master cylinder push rod?

 

Before you think about changing the clutch, adjust the pushrod as "Offroadnutz" mentioned. I had trouble shifting to first, to third and reverse; changed the shift seat seal, bled the clutch and almost took the transmission apart. Good thing I didn't, all I had to do was adjust the clutch pushrod at the pedal.

 

Clutch pedal adjustment: yotatech.com/forums/f116/clutch-pedal-adjustment-w-pics-291259/

 

Thank you guys!
I did adjusted the master cylinder push rod play. It has to be between 1.0mm and 5.0mm. It's 3.0mm, so that's good.
My 4R clutch pedal height's 150mm from the carpet. The FSM says 155.5mm from the asphalt sheet, and 157.5mm from the floor panel. It should be, at least, 5mm higher. Could that be the problem?

 

it could be; might not have enough travel arc to fully push the rod to disengage the clutch.

 

DO check for a crack in the clutch bracket. https://www.yotatech.com/forums/f116...fatigue-32667/

 

I'm going to adjust the pedal height...

... and check for cracks in the clutch bracket and I'll report back.

Thank you guys.

 

Update:
Clutch pedal's height 5mm higher solved the problem.
Thank you very much!