Hey man. Welcome to the forums.
First off, i'm not sure what your situation is so i'll try to answer your question before I suggest a different plan altogether.
I haven't seen a lot of custom boxes for the 05 mustang but then again I haven't looked that much. I'm more of a traditional square box guy and the mustangs trunk isn't that big to begin with so taking up most of the space isn't that big of a deal to me. If you want my opinion, box-wise, then I say that the simpler you go, the better. I run a 12" Alpine Type-R in a square sealed single-sub box. Its a generic square box that I paid like $40 for at Circuit City like 5 years ago. It lasted through my last setup (12" Alpine Type-E, 200w) and its holding strong with my new Type-R.
I've heard of people having their Type-R 12's 'jump' out of their box. In other words, pull the screws out because its hitting so hard. My box is holding strong after 4 months of Type-R abuse.
Now that that is said, i'd like to address your situation with the Type-X. I've done my fair share of stereo listening and I tell you now that I can't tell the difference between the Type-X and the Type-R. Flavor-wise they're so incredibly similar that its scary. Power-wise the Type-R will literally give you headaches. If you're really looking for power you could get 2 Type-R's for the price of 1 Type-X and out hit the X no problem. Remember that more subs move more air so 2 12's @ 250w each is going to make more volume than 1 12" at 500w,
if the subs are run at their optimum RMS rating.
Running your stuff at your optimum RMS rating is key to having a loud and good sounding setup. A 400w run at 400w will sound better and hit harder than a 500w sub run at 400w. Don't forget that with the higher ratings of the Type-X you're going to spend a small fortune on an amp to match those numbers.
Don't be afraid to run at 2ohms. My amp puts out 300w@4ohms and 500w@2ohms. There's no audible difference between 2 ohms and 4 ohms so get a dual 4 ohm sub and wire it in parallel for a 2ohm load. It'll help you save a few bucks on your amp.
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Black 2005 Mustang v6, 5 speed, IUP, EUP and Leather.
Razzi 1/4 window scoops, Mustang GT Sway Bars, Flowmaster American Thunder Single Exhaust, Clear Front Turn Signal Lenses, Demolet CAI, X-cal2 91 tune, Hurst Comp/Plus Shifter, FRPP T-Lock, Ford 3.73 gears