It sounds like you had the same problem I did. The instructions weren't clear enough. I almost did all the same things you did, until I took off the weather strips. The bolt holes are there and are the right separation width so no modifications need to be made to the ARB roof rack or supports. The support arms work if you get them in the right order. The middle two are shorter than the outer arms. It takes some experimenting on the rig to find the right configuration.
Bottom line is that the ARB roof rack fits great on the US 100s. The instructions are poor at best. It sounds like you went to a lot more work than you needed to. I almost did the same thing. I wrote a post about it last year.
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Dwon
http://www.gshot.com
2001 UZJ100 (07-29-2007)

Toyo Open Country MT 285.75R16 (09-01-2007)

ARB Bull Bar (09-13-07)

ARB Roof Rack (09-13-07)

IPF Lights (09-13-07)

OME Firm Valve Shocks (09-14-07)

OME Springs / Tbars & Slee Drop Diff (09-14-07)