I took off the entire roof plastic set-up as soon as I got it home...once gone, the sun roof works, etc.
The sun roofs that steal head room are the sliding ones, this one just pivots up like a vent window...so there's no loss in head room.
I think the slight color variation you mention on '01's, etc... is from fading in the sunlight/weather, etc....there are plastic treatments you can apply to protect it from further damage.
(I can't see from the picture what you mean though)
So - if you mean something else, look underneath at the mounting points for the bumper, and see if there's any sign of tweaking/damage (Replaced parts, etc...)
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- TJ
2001 Xterra '03 VG33, SE 5 spd, 305/70/16's, Revolvers, UBSkidderz, Doubled AAL's, 3"SL/2"BL, winch/bumpers, skids, sliders, OBA, Snorkel, pine stripes....
Friends don't let friends drive stock.
http://www.gifsoup.com/view/501230/tj-tackling-crawlers-ridge-o.gif