Hi there. If it's any help, the MFD bridge pickup on my S-500 won't go as high as the spec suggests either. You basically run out of turns on the screw and there is a spring on the underside of the pickup which stops the pickup going any higher. This stressed me out greatly until I realised the MFD pickups sounded better set LOWER than recommended anyway (at least to my ears).
It sounds like you have done everything else correctly.
After living with the MFD pickups for a while, I decided I liked a vintage tone better and put some G&L Legacy pickups in. They wouldn't go to the recommended height either but, like the MFD's, sound better set lower anyway. Any third party stratocaster pickup e.g. Texas Specials should fit in there too if you go that route.
Be sure to post up some pics if you get a chance. We love to drool over G&L's on this forum!