David,
Welcome to the message board! A 400+ gallon tank can be an absolute dream to own if it's well researched before purchasing, or it can have the potential to be a complete nightmare if it's put together on impulse.
I'm in nearly the same boat as you right now. I own a 29g reef and am about to upgrade to a reef in the 300 gallon range. This tank was originally planned to be setup last summer, but some hurdles got in the way. That gave me alot of time to research and check out quite a few local systems sized like the one I am planning on setting up. Seeing other systems in action and talking with their owners about their likes and dislikes was the most valuable info I collected. I fully intended to piece a system together, but in the end, I found a 300g complete reef setup for sale locally at a price too good to pass up (I'm actually picking everything up this weekend).
With that said, I'll take a stab at your questions with the perspective of someone about to set up a large system.
First, the tank will dictate how the rest of the system will be setup. Personally, I think you're making a wise choice going with acrylic in a tank this large; with solvent welding, a well built acrylic tank should last a lifetime.
You didn't mention what you plan on keeping, but from everyone I've spoken with, a tank taller than 30" or so is very difficult to work on, let alone provide enough light for. The consensus is that a tank with a front to back dimension greater than the height is much easier to aquascape and looks more natural.
Plus, a 48" height would require acrylic in the area of 2" thick, which would be extremely heavy and expensive. Also, consider the logistics of the manufacturer getting the tank to you. Shipping a 1/2 ton tank across the country is not cheap.
As I mentioned earlier, I picked up a used system locally, but had shopped around with many custom tank builders. Personally, I am not comfortable with a glass tank larger than 200 gallons, so the choice for me was acrylic.
Here is a list of acrylic manufacturers I got quotes from and some general opinions of them (note: I've seen most manufacturer's tanks in person):
-Tenecor (a reputable acrylic manufacturer, but their tanks are mass produced and not as nice as some others on the market; custom work is expensive; their Marine Ready setups tend to be undersized and overpriced)
-Envision Acrylics (best custom builder in my opinion; bends over backwards for its customers; decent prices; everyone I've spoken with said this is the builder to go with if at all possible)
-Midwest Custom Aquariums (tanks aren't built as strong as other builders; good prices)
-Precision Clarity (I spoke with two owners of these tanks; one had an outstanding experience, the other had nothing but nightmares)
-Aquaquarium (small outfit local to me, but ships nationally; builds a solid tank and doesn't charge an arm and a leg for custom work; good prices; this is the builder I planned on going with before I found the used system)
Ultimately, I've found that the nicest systems are typically put together piece by piece by the owner after lots of research.