For removing buttons, you will have to comment out the relevent lines in the .skin file. This will cause those buttons not to be shown. The other buttons you will have to edit within the psd file.
To change the size/shape, first "hide" the layer style, so you have a flat grey "button". Use the colour dropper to get that colour, and then move/redraw your buttons to the size/place you want. Enable the layer style again, and then edit the layer style, and change the colour for "Outer Glow" to what you want it to be.
Just remember that the 800x600 ones are stretched in the vertical plane. I found it MUCH easier to change things on the 848x480 PSD files then resize (width 94.3% and height 125%)/save as a jpg.
If you want any help, I'll be on AIM/MSN today (details in profile), i'll be glad to help