You can get the whole window out in one shot if you leave it in the sun then use something to pry the frame out of the roof... comes out like butter.
You have to remove the whole frame first before doing anything else... it come apart pretty easily after that, just a bit of a pain getting the glass out...

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