Hey Bud i have serviced many manual trans clutches on import and mustangs ,and mopars i have found even with the correct alignment tool they can be stuborn to get seated the way i do it and it works 99.9% of the time if you have checked everything else as it seams you have .
Have a helper rotate the engine from the front crank bolt with a ratchet while you push the trans in and wigle it up and down verticaly as you are pushing . also two home made studs installed in the bell housing to trans will help big time with this process . cj