Judging by what you have done to your truck, you will have no problems.

There is also a string in the butyl rubber holding the window on that you can pull, but i didn't need it. Any pics of the fixed roof?

89 4Runner
3" BL, M/T locks, 33"bfg mt, bilstein, Kayline, tubebumper, toyotafiberglass panels
TBI: Elocker,3.4 w/ORS,b+b,S2Sstg2cams,arias pistons,P+P intake,TRDs/c,URDpullies+7th,downey headers,MAPECU2,WEGO WB, SupraMAF,walboro255,stg4clutch, EPaOo2 sim