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To build a "proper" 4 link setup you're looking at $2,000 in materials alone and you can count on that much in labor. This is not even getting into springs or coilovers or whichever route you'd choose to go. Don't get me wrong, I think 4 link is the shizzle but it will eat up half your total budget and won't be needed for what you plan to do. If that shop tells you they can build a 4 link suspension for under $5K they don't know what they're doing and I'd definitely recommend going elsewhere.
I built my own rear shackles and though I don't have any pics at the moment they're much heavier than the stock shackles. I could put a fair amount of weight in the bed even with the shackle flip and never have to worry about it. Take a look at my gallery and Proeliator's to give you some ideas on suspension systems that can be built for a good amount of functional lift with no banana springs. He's got 18" of lift with stock F350 springs. I'm using 4" springs in the rear and 6" in the front of my truck. You should be able to get leaf springs for under $1000 and have custom hangers and all that junk built for about another $1000. Btw, I've seen several guys run the ladderbar/trac bar setup like they talked to you about. These work well but I'd get my own heim joints and insist they use the brand you choose. Use Evolution heims, they're $50 each and are about the stongest out there. I can find you the contact info if you need it. They'll still need to fab custom hangers for the front of the truck.
Not that you have to cut your fenders but you're looking at having your rockers even with the top of your tires if you don't. This puts them at 52" which is way up there. I don't think this is necessarily a bad thing but it can make your truck a little unstable off road and pretty fenders don't stay pretty if you flop on your side. You might check into Bushwacker cutout flares that will allow you to cut 2.5" out of the fenders and still have a clean finished look.
I may do the cutouts. I just didn't want to trim until I had a couple inches of fender left above the tire. 2.5" for a fender cutout would be ok I guess. I guess I could always cut them and put the flares on. If I don't like it I'll just replace the fenders and figure something else out. I'm going to talk to the shop later this week about the lift and what I want to use to hang the rockwells. I may just throw a crane cam in the motor and maybe a bit of the funny gas for now. That way I can deal with the Rockwells/tires and how to hang them. I would rather have a safe off road suspension then a blower sticking out the hood. On another note for those who have seen my only pic in my gallery and think I should work on the body I have located a very clean bed for $275. Next week I will head down and pic it up. Then I have to redrill the mount holes cause I have a highboy and the holes are different then the regular beds.
You don't need to do the body work like others and yourself said first. Get done what needs to be done, because you know something is going to happen to the truck, either many scratches that would mess up a new paint job or somthing else.
Get all the important stuff done first. Drivetrain, suspension, wheels and tires and IF you have money left over you could be on a cheap paint job.
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