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Yes, the input shaft is slightly shorter. I believe Glazier's Mustang Barn sells an extended pilot bushing for this specific purpose, however, and it should work fine with that 3sp toplaoder bellhousing.
You can also buy the proper shaft. Installation requires TOTAL dismantling of the tranny, but it's not that hard and it isn't a bad idea to go ahead and rebuild the thing while it's out.
how important is it to have the tailhousing from that car? as im getting a custom driveshaft mostlikely anyways... and it seems that it is the right tail housing
No, the tailhousing is not correct. The shifter mount on the Mustang tailhousings are on the far rear, whereas the Galaxie tailhousing is going to have the shifter mounted more towards the middle or front of the tailhousing. That said, it's not difficult to swap tailhousings if you happen to have one lying around.