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I can't say what the policy is for 2000's but my 99 F350cc 4x4 is going to be lowered by 2 inches shortly. I called the Ford mechanic at my local dealership and told him that some 5th wheels I'm looking at are too short by ~ 2 inches for my truck to get under the hitch. He said that Ford will do a 1 time adjustment by either substituting 2 inch spacers (mine are about 4 inches tall) or removing the spacers entirely. He says there are some parts (hoses of some sort) that are also swapped out at the same time. I'm going to the dealer today so they can get some numbers from the truck to order the correct parts. I'm going to try to talk them into letting me keep the old parts in case I ever decide to raise the front end ~ 2 inches to match the existing rear height.
We are talking 4x4's here. They are NOT lowering free of charge for 2000. But not all models use the 4 inch blocks. The single rear wheel crew cabs do have 4 inches. Most of the new supercabs seem to have 2 inches. The owners manual for the 2000 gives the heights for all models under the specification page. This is the easiest way to figure it out, as some trucks are two inches taller than others. If you let me know which truck you are looking at I can look it up (Monday at the earliest) , but dealer should have this. If you are wondering because of a 5th wheel tow/clearance, I think it will be cheaper to have the 5th's axles flipped. Good luck.
2000 F250 have the 2" blocks in the rear so these don't have to be lowerd. 2000 F350 DRW have the 2" blocks also. 2000 F350 SRW have the 4" blocks. Ford will not lower the F350 SRW for free as per a previous TSB (the number of which escapes me at this moment but I can find it if need be).