The clutch seems to grab just fine although I always seem to have to run the shifter into 2nd to get it into first at a stop. I know the engine was replaced 2 years/5000 miles ago so I would think the clutch would be intact. Thoughts?

On the easy side of things your clutch could just need to be bled

sometimes you can adjust the return tension of the pedal

worst case, you need a new clutch master or slave - it's best to replace them as a pair.

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This definatly isnt a TO bearing problem.

I am thinking I may want to change the entire tranny out eventually since it'd be cheaper than overhauling it. Since I live in the city and don't have a garage for my use I will probably be put into a situation where i have to take it to a mechanic. How many hours do they charge for a tranny swap, I'm thinking 6. This wont happen for many months yet. thoughts?

Replacing a trans that you have no idea where its been can be costly. It may even be worse than the one you have now, and you wont know it until you drive the car.
Just something to think about.

Could be unrelated, but who knows.

Don't let the shop tell you it's only one of the 2 that's bad. TRUST ME! Been There, Done That. Usually the slave starts to stick, causing extra pressure ont he master. Master then blows it's seals. Guess what happens when you replace only the master? A few weks or months later the sticky slave causes the new master to blow again or the slave finally totally dies. Do BOTH!

Anyone made a write up on how to do this? I want to try to bleed it before I get replacements.