Sounds like you'll have to center the bellhousing to the crankshaft's end . There are many vidoes that outline the process on YouTube . I looked at quite a few before I began . Summit Racing has the dial indicator you'll need- unless you have one . I'd call them at their Tech choice on the phone . I have a '07 V6 & 5 speed manual , I questioned the alignment & found the stock locating pins on the back of the block didn't allow for the needed adjustment to get good alignment , I had a local machinist friend machine new pins I cut that essentially are eccentric , but adjustable . Once I found where the high/low was , I set them accordingly , using a Fine Sharpie Pen that I'd marked for ' high & low ' . I nailed the runout on the first time - frankly was amazed it happened - I expected at least a few ' take er off's & out er back on's ' . My bellhousing had been .007 out , with stock pins . In your case , check out Summit for a ' Quick Time ' bellhousing , I was told by some Ford folks that they made an install & centering task much easier . You have a C4 , so you must have an earlier 'stang , sometimes - as I've read - one can drill the mount & pin holes slightly oversize and adjust to suit . I balked at the idea myself , especially at the locating pin holes- but others have had success . I can say I got lucky ! I had room enough with all holes ' as stock ' but using the eccentric pins . There are eccentric pins available from quite a few sources - make sure ya index the high/low so you can see the mark with the bellhousing in place ( usually you can - if the hole isn't drilled all the way thru , you likely can ( carefully ) drill it thru so you can affirm they haven't moved during the trial fit . On mine , I'm going back into the clutch assy to replace a hydraulic line's holder - it's plastic - somehow the clip's snap tang came undone . Also I want to check the roller bearing in the crank end & the tranny input shaft's 'nose' that stick in there & check the wear marks and see if my work is okay ; there's normally a wear mark on it where the roller bearing rides on the input shaft . If the mark- or marks are equal , or nearly so- It's all good . This job is/can be one fickle dickle stick , but it was at least interesting . I'd try the stock bellhousing first & see what ya have to work with , and be ready to go from there . Good Luck & don't hesitate to call the Tech Guy at Summit , they've never steered me wrong .