I have had different experience then a few of the guys that have posted with lowering OBS trucks. I just sold a 96 Ext cab that was lowered 5/8. I made a custom notch and used Belltech spindles, cut front coils, Belltech flip, Belltech carrier bearing relocator modified to not cut the cab, Belltech shackles, Belltech shock extenders, Belltech front Nitro 2 shocks, Monroe rear shocks and a modified NBS McGaughys helper bag kit. Even with that large amount of drop I did not have to touch the bed floor crossmemeber. Yeah, some times the pumkin hit it but it wasn't worth ruining the bed. I also did not have to relocate any part of the brake lines on the rear end.
Here's a few quick pics to give you an idea of the drop. It is very driver friendly if you know how to drive a lowered vehicle.
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I just picked up a 99 Tahoe and my lowering parts should be in the first of this week, I am excited to get it sitting right. Good luck with your build and I look forward to seeing the progress