complicated clutch problem

I have been working on my clutch over the past couple of weeks. First, I bled the heck out of it with a Foodsaver vacuum suction; and I also know that the problem isn't the master cylinder.
Try and picture this: the master cylinder in the back of the car has a "plunger" that goes into it. When you press in the clutch, this plunger goes out which engages the clutch. Well, I found out that the plunger just needs to be primed by something. So, I cut a dowel to the appropriate length (it took much time and precise measuring) to get it just right. Then I had someone push in the clutch while I stuck the dowel onto the far screw that holds the plunger and master cylinder. When the cluch released, the plunger rested on that dowel, and it worked, now I have a nice, reflexive clutch.
The only problem is, for some reason, every other time or so when I start the engine, it is very bogged down and "bumpy" and will die eventually. However, I don't smell the clutch burning up. So I push in and hold the gas until the engine responds smoothly, then it idles fine.
So one, I want to know what the problem could be, and also, the clutch works well now, but every once in a while I still smell it burning up. As you've read, I have fine tuned that dowel to get it in just the right spot, so what could the problem be (it isn't the master cylinder)?

I just wanted to add that when i was talking about the "plunger," and referring to it as the master cylinder, I meant the slave cylinder. But I was still referring to the master cylinder in saying it didn't need to be replaced.

The poor cold idle doesn't sound like it's related to the clutch in any way. It could be a number of things, from a vacuum leak, to bad plugs, a clogged fuel filter, or malfunctioning sensors. I'd start with a basic tune up (plugs, wires, cap, rotor, fuel filter and air cleaner) check all vacuum hoses for pinholes, then check for proper fuel pressure, as a failing fuel pump could cause what you described. If the problem still doesn't go away, the issue is probably in the EFI system somewhere, it's pretty hard to diagnose without getting a printout of all sensor values at cold startup from a diagnostic scan tool. If I had to take a pure educated guess, I'd say map sensor, but don't hold me to it.

As for the clutch, it sounds like the slave cylinder is buying the farm, replace it and you should be fine.

Alright, well I have already given it a homemade tune-up, but still did same as shop would do- new plugs, new cap, rotor was fine, bought tune-up in a bottle to clean the fuel filter (I don't know how well those things work).
I'll look into your suggestion with the map sensor, and consider the replacement of the slave cylinder after doing some more research. thanks.