1. What do I do for a pan. The present one is copper but even if I can save it it will be too small.
You can't save the pan, do a new one. Take a look at the Schluter Systems KERDI showers kits.
http://www.schlutersystems.com2. I bought glass tiles for the whole shower walls and ceiling what to I use to put it up with (? White thinset).
When using glass tile it is best to go by the recommendations of the tile manufacturer when choosing a proper adhesive, they will have a list of products they recommend.
I will use either durock or hardybacker (whichever you think is better
One is as good as the other. Hardibacker is probably better for small glass mosaic tiles.
3. I am looking for a black tile for the floor of the shower, but can only find a glass tile. Would that work or would it be dangerous and slippery
Glass would absolutely be a safety issue for a shower floor, I wouldn't use it there. There are black tiles available. I am using some on a job now. Use nothing bigger than 3" tile for the sloped shower floor.
4. I am putting a bench across the back of the shower
Too much span can allow deflection. How big is the shower? Look at the metal "Better Bench".
http://www.innoviscorp.com I also want to put a niche in the wall for Shampoo etc. I have looked at the thread on that, but don't quite understand the best way to do this.
Use a pre-made niche. The above website also offers a great niche product. There are many others also.
5. The bathroom itself is very small only 6X6 with a pocket door. I am taking all the present tiles down, and wonder where the pocket door wall is if I should use 3/4 plywood since I do want to tile part of that wall.
Drywall (only) is all that is required for tiling over a pocket door cavity. Use MR (moisture resistant) drywall.
6. I also am using an IKEA sink which I love as it is a porceline 31" wide and only 16" deep trough sink with full shelf behind, but want to know if anyone has a suggestion for their base cabinet to make it more waterproof since I believe it may be a melamine foiled particle board.
Those particle board bases can be bad news. You can use a liquid waterproofing for the top if you intend to tile the vanity top. There is more to it than what has been mentioned so far.

I may have a few more questions to ask, but for now I hope you can help me with these. THANKS IN ADVANCE!
Ask away! Someone knowledgeable is always here daily.
[Edited by Bud Cline Tile on Sun, Dec 6, 2009 at 9:26 am CST]