I think the locking pin you're referring to is to lock the transmission into 3rd and the shifter into 4th while removing the gearbox and then locking the shifter into 3rd once the box is back in to align the shifter with the box?
If so, a set of allen keys will work well, you can find a size that's large enough to accurately locate the shifter and trans linkage yet easy to install and remove.
Honestly, I'd think a failing slave cylinder would give you different symptoms, such as a fluid leak. Still, your basic symptoms do sound a bit like air in the hydraulic system for the clutch.
Another possibility is that there is some debris in the clutch pressure plate causing some issues. If you do drop the transmission, I'd highly suggest you take the time to pull the pressure plate and clutch disk and five them a good inspection.
Bleeding the clutch can be a real chore, either if air in the system is the problem or if you remove the transmission and reinstall. Getting all the air out of the slave cylinder is nearly a must before you reinstall, and an EZ Bleeder with a hose returning to the fluid reservoir will make the rest of the bleeding much easier.
The clutch has a small, slow filling side reservoir inside the main fluid reservoir. It's VERY easy to drain all the fluid from the clutch's portion of the reservoir with the rest of the reservoir seemingly still full.
