I had a Marlin heavy duty trans put in my truck a few months ago and the mechanic didn't put the rubber boot back on the slave cylinder. I drove to Montana in the snow which I think might have caused it to go out. Now, it takes a few tries to put it in first and second is hard, although every gear is kind of notchy. Does this sound like the slave cylinder? I'm thinking I might need to get another one and order a rubber boot from toyota. Am I guessing right? 86 4Runner 223,000 miles Ranchos Marlin HD trans, ceramic clutch kit rest stock

 

If it feels like you are trying to shift without pushing the clutch, then it could be the slave cylinder. I would think that you could rebuild them like brake slave cylinders for only a few dollars. The kit would probably include the rubber boot.

 

Have a look at the slave cylinder while someone pushes the clutch pedal for you. You should be able to see if the rod is moving out properly. And if it's not I wouldn't bother trying to rebuild it, rebuilt slave cylinders are cheap.
If you still have the original master on your clutch you might want to think about doing that at the same time. From my experience when one goes the other isn't far behind.

 

Both of the cylinders are new with the transmision, also new cltutch kit and pressure plate. A local mechanic yesterday said he thought it was my synchros but I just bought the tranny from Marlin like 6,000 miles ago. I think I'm going to give marlin a call. I looked at the slave cylinder and as far as I can tell it's working.