I did something similar but with a slightly different setup (351W, toploader, diaphram clutch, stock 66 bellhousing, Ford Racing flywheel).
My flywheel (part number M-6375-A302, 157 tooth, 28 oz-in balance) has two sets of clutch mounting holes drilled and tapped (from the factory). One set (the two holes on either side of and closest to each of the three alignment dowel holes) was the metric thread and was used for the late model clutches. The other set of holes were SAE threads and were used for the stock 10" clutches. The alignment dowels are not used with the 10" clutches.
I was using a McCleod clutch that would have been a stock-type replacement for that model year 289, but which was a diaphram style rather than the 3-finger style. I bought the clutch at John's Mustang in Houston (this was years ago) but I know other companies make them and there could be one available locally at your auto parts store. National Parts Depot and Mustangs Unlimited both list replacement style clutches that should work for your application - assuming your flywheel has the SAE holes as mine does.
If you do not know whether the flywheel you're considering has the two sets of holes, Ford Racing does have a tech line and they do seem to know their stuff. It's (800) FORD788 (800 367-3788)
Hope this was of some help.