A number of people here remove the AC system but leave the evaporator in place. I removed the evap as well and modified the HVAC box so that I could retain my heat functions but still gain a lot of space in the engine bay.
http://www.vilipend.com/~frrax/Evaporator
I had to leave a few inches of material of the evap box to allow proper air flow from the blower motor. I could have trimmed a bit more off. I would rather have made a flat panel across the whole area, but it would leave VERY little space for the air to flow through from the blower chamber. If you take yours apart you'll see what I mean.
I made the cover out of scrap steel flashing I got from a friend. It was tight in some spots installing the rivets.

 

Thats a good idea. I just beat all of it out with a hammer and made a flat plate without the heater.