I'm trying to install an amd left quarter on a 68 roadrunner. The window channel won't line up with original roof. See pic. Anyone else had this issue? Any suggestions?

Love them 68 MOPARS! GTS 340 auto, Charger R/T 440 4-speed, Superbee 383 auto, GTX 440 auto, D100 (new front frame 5.7 hemi - in process), Formula S 340 4-Speed A/C (it's green), 383 auto Roadrunner (maybe a hemi - waiting) and a 68 W200 Power Wagon. Drivers: 07 Cummins and 14 Ecodiesel 4x4.