Hey SGT Fast, i've remedied the problem through trimming of the fenders themselves. I started this a while back to try to better understand exactly why a drop lift is considered bad. I got a few useful answers and some not.
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Bigg50 - Sorry I didn't see this earlier and glad to hear you remedied your problem. I read the first few pages and then skimmed to the end, but it appears that many folks here don't really understand or haven't seen how these "drop bracket" lifts work. Please don't anyone get me wrong because I know a suspension lift isn't right for everyone, but I feel the "because it's a Raptor" is just a sheep answer that keeps getting regurgitated by people that don't really have an educated answer.
I've ran this style lift in the past on different trucks and havent had any problems with them when run hard... especially the Fabtech brand. Yes, some brands are pretty ****** and use ball joint and coilover spacers to achieve lift, but retain front IFS geometry and simply throw a larger lift block, or even worse stack a lift block on top the factory block, under the rear leaf spring to gain height; these are typically referred to as "Stage 1" lifts and I agree that they are strictly for pavement queens who only have a desire to fit larger tires. A Raptor with stock rear leaf springs wheel hops bad enough... I couldn't imagine what would happen with stacked rear lift blocks and ball joint spacers would surely fail pretty prematurely.
CROSSMEMBERS:
A good lift (stage 2+) will use drop bracket crossmembers to relocate the frame attachment points for the lower control arms. I'm not sure about the Fabtech lift for the Raptor, but the Fabtech lift for a 2004+ regular F-150 used 1/4" thick drop-crossmembers w/ all welds receiving shot peening treatment; this is significantly thicker than the OE frame it's attaching to.
STEERING KNUCKLES:
A good lift company will include replacement steering knuckles (spindles) to span the new increased gap between the stock upper control arm/ball joint and the stock lower control arm/ball joint that's been lowered because of the drop crossmember attachment point. Cheap lifts use ball joint spacers on top of the OE knuckle to accomplish this = not good. Also, the new steering knuckle will relocate the outer tie rod attachment to keep factory steering geometry.
Note: Because of the replacement steering knuckles and added frame mounted crossmembers, you will retain all factory steering, CV, and axle geometry.
FRONT SHOCKS/SPRINGS:
Good lift kits will replace the front OE shocks/springs and/or coilovers with a longer unit. Because you're not gaining suspension travel with this type of lift, the shocks are usually custom made by the lift manufacturer to employ a longer shock body to span the new longer gap between the frame and lower control arm attachment point. The cheap lifts simply bolt a spacer, in this case 4", on top of the factory coilover to fill the gap. Typically I'd stay away from spacers at all cost, but because most shocks included with a lift kit won't be as good as even a stock Raptor shock, I may consider the spacer route if the spacer is well made. The best thing to do would be to replace your front coilovers with something longer and aftermarket even though the longer stroke of this new coilover will be somewhat wasted.
REAR SHOCKS/SPRINGS:
All kits are going to include new rear shocks, but like the front, they probably won't be as good as stock Raptor shocks; you'd be better off taking this as an opportunity to upgrade your shocks to a nice longer 3.0. Most kits will include a new taller lift block to replace your factory lift block with and the cheap kits may even give you a small block to stack on top of your factory lift block. I'd stay away from both methods and buy new rear leaf springs with the proper arch to get your rear height where you want it.
I think these bolt on, drop bracket, style suspension lifts get a bad name because there are so many street queens out there running cheap "stage 1" style kits for the sole purpose of only stuffing some bigger tires under the truck. Things I mentioned above in good quality lifts along with adding longer flexible brake lines, properly relocating and extending wiring harnesses (ABS), vacuum lines, and axle vent tubes can and will go a long way. I'm currently running my Raptor with stock shocks at mid-perch, but speaking only to the front suspension, I'd be more comfortable running my truck with a 4" Fabtech lift with proper shocks than I would be running stock shocks at top-perch. FACT: Your front tie rods, CV shafts, ball joints, and control arm pivots will last MUCH longer with a 4" Fabtech lift than they would if stock at mid or top perch.