If it were me, I think I'd also install the software on the computer I was going to use. When not working on the actual build, be learning the software.
On building your table frame just be careful you don't warp your frame rails when welding up. It's really easy to "over weld".
I don't know what their plans call for as far as thickness on the box tubing but if you want the table more sturdy. I'd opt to go up in wall thickness of the tubing rather than larger size square.
Another thing that comes to mind is height of the table. Again I don't know what their plans call for but you may want to think about short legs to lowering the bed height to make loading & unloading the table easier.
Even though You will have a set of plans, & I'd try not to modify them any more than necessary. Look & read through others build logs. You'll get lots of ideas there.
Here is a link to a TM 1 build log. Yours is a 2 & gantry is pretty much pre built but there will most likely be lots of other similaritys. http://www.cnczone.com/forums/showthread.php?t=32058 (My Torchmate 1 build log)
Welcome & good Luck.