Toyota Repair Problems? Ask a Mechanic for Answers ASAP
Hello the first thing to do is bleed the clutch hydraulics and ensure that you replenish the all fluid in the system and get any trapped air out I favour having a clear hose from the nipple to a jar 1/2 full of old fluid and with the nipple closed your assistant pushes the pedal up and down a few times, then holds it down whilst you then crack open the nipple and close it again whilst fluid is still flowing. If this doesn't help then next check the gear linkage for any worn bushes or pivots as any lost motion means reduced effort at the gearbox and replace as necessary. Ideally have your assistant move the gear lever with you watching the linkage and see if you can spot where there is any excessive play or lost motion.
If its a cable type linkage check along the cable lengths for any damage or signs of heavy wear / fretting, if you find any replace the cable. There may be some adjustment on the cable tension at the gearbox end (depending on the year) and the cable should be tensioned so there is a minimum of slack but not so its taught Then check gearbox oil levels are OK and consider changing the oil again. I can strongly recommend the use of Castrol Syntrans 75W90 (was called SMX-S) as I've known it help with shift issues on many manual gearboxes
If you still have issues with the hydraulics and its good after bleeding but then gets worse after a few days / hours, then I'd try leaving the clutch pedal held down overnight by bracing the pedal against the seat base with a piece of wood or similar, this is to try and force the seals inside the slave to take a set in the right orientation as over time they can shrink and draw air back in when you take your foot off the pedal.
This shrinkage isn't enough to leak any fluid but the gap is big enough to draw air in (gas being harder to seal than fluid) if this doesn't work I'm sorry to say that the slave cylinder is going to need changing.
The clutch is working fine, and all other suggestions you have made seem to be OK, as an addition I have noted there are some strange outcomes when I do the following.