Hey - someone else who roots for a team who once had Shaq. Go, (somewhat helpless) Magic
Please take a gander at www.rexgrigg.com
. It has some good concise, straight forward info on what all you'll need. It sounds like you are well on your way.
The 2x96w CF is some sweet lighting. I have a 46g and really like it (you might want to check out my photo album and others as well). I can't remember, but assuming the 40g is also 36" wide, you might be able to get slightly better light distribution in the front corners of the tank. I seem to recall the 40g having some nice dimensions for a planted tank, and it might be a bit cheaper. But, the bowed fronts have a sweet look. So either is likely very good.
As to substrate, I too use flourite. It I were to start again, I might go with Eco-complete. The black is a nicer contrast, and the rinsing of flourite can get old in a hurry.
If you can spring the extra $200 or so for pressuring CO2, GO FOR IT! It's might easier to maintain good, stable levels and saves a bunch of time. After the initial outlay, refilling tanks in only around $10, and with the time savings, it pays for itself.
With a 40g or bigger, pressurized CO2 and a canister filter, go with an inline, external reactor. You can DIY one for $10-$20 or you can search around for other ones (I think Aquamedic has a decent one).
Sounds like you've got the basic idea down and just need to fill out a few details. Good luck, and welcome to the boards!