I've owned a FTGT, an MST1, and a Drake, and I'm running the Drake now. The Mugen handled well, but required a few custom mods to get it to that point (dremeled GT diff rings, drilled pistons, I swapped the axles out for CVD's, and I changed the brake linkage). My main problem with the Mugen was that the axles do really suck, and there's pretty much no parts support near me for it (had to order everything from Nitrohouse).
I really like the XXXNT. For my driving style, it's the truck to have. It doesn't need to be driven as hard as the GT (the Losi favors a smoother driving style, while the GT favors an aggressive driving style). As long as you build the diff right (and don't use the white lube that comes with the truck..use AE grease) and adjust it right, it will last forever. The Losi definitely isn't as durable as the GT, but that's also to be expected, since the Losi is an all graphite truck while the GT only has graphite towers. The NT isn't as easy to work on as the GT, by far.
The FTGT was the first gas truck I owned, and for tracks with big jumps where the truck will be abused nonstop, the GT is probably the truck to get. AE is known for their trannies, and the GT is no exception. The GT requires a little more patience with setup (takes a bit longer to get a good setup, at least on tighter tracks), and the shocks seemed to need more frequent rebuilds for me. However, it's reliable, handles well (once you get the hot setup down), very durable, and easy to find parts for and work on. Solid choice, and probably what I would recommend for a track with large 1/8 style jumps.
As far as clutches go, for the Mugen and the Losi, I'd just leave the stock clutches in there (that's what I ran/run). For the GT, I'd recommend the MIP 4-n-1 clutch. For pipes, the Drake pipe is awesome, and the FTGT pipe is great, too. For hopups, tell us which truck you decide on, then I'll reply about that.
For engines, there are lots of choices. The OS CVR and TR are solid choices, but most people go for NovaRossi's or Piccos. If you just want a smooth, reliable engine, the CVR would be great (and if you can find it, they make a short shaft version for the GT...there's a short shaft TR, too). I run an MT12 with OS 10ER rotary carb in my NT (took it from my MST1), and I love it. For a bigger track, I'd probably recommend something like that, or a Picco Wasp. I've never driven a Picco, but I have heard that they are smooth on the bottom end, but scream on the top end. NovaRossi's scream, too, but they're not quite as smooth on the bottom end.
For most of this, however, it's all personal preference. See if you can drive some people's trucks, and if possible try trucks with different engines, too. A big part of picking the truck and engine is your driving style, so try some out and see which you like best.
Feel free to IM me if you have any more questions.