Well, that's a hard question to answer. The reason I say custom 4 link is because I have no choice now if I ever wanted to do a 4 link. I've got TNT stiffeners, and T&J stiffeners over the top of them. There isn't a cross member that will mount up now. So if I did one I would have to weld it all together. Realistically though I'll probably never go long arm, I get just as much out of my short arm kit with drop brackets. The only down side I see to short arms it the arc path during travel, with 10" it's not a big deal, but I think with anything more it'll become a problem.
I can't say that I'd do anything differently from the get go, as it helped me learn my Jeep inside and out and taught me what worked and what didn't. I am however now going a completely different route, I'll be running a coilover up front with a few tweaks here and there, it'll be tough but hopefully worth it.
As for the rear, I thought about running spring under, and may still, but for the time being I'll just be running some Deavers SOA.
Words to the wise though, things that I've learned:
1.) Frame stiffening is your friend, it'll make a night and day difference on the feel of your truck, you'll actually be able to feel suspension. I liked the TNT's but noticed the most difference when I added the T&J's on top of them, as well as the TMR front frame plates. I think the combination of them helps.
2.) If you're going to go long arm, do it before you do any frame stiffening, and if you're going to do it then do it right. Go with a true 4 link kit like the full traction kit. It's spendy but worth it.
3.) Air bumps are your friend. Honestly one of the best mods I've done suspension wise.
4.) Strengthen your coil bucket / mount. The sheet metal around mine is bending, and now my bump stop is pointing forward from taking a beating.