The 5 bolt bellhousing was a pre '65 thing. Since the o/p has a 1968 model year engine, that's not a concern here, but a good point to bring up as that could pose an unfortunate issue.

289/302 was a running change during the 1968 model year, depending on model and availability.

For overdrive automatic transmissions, the best ones for this application will be an AOD from the late 80's early 90's from any model Ford that would have had a 302 or 351W (Crown Vic, Thunderbird, Mustang, etc.). Those have the best updates before they went to electronic control (AODE). That just opens up a huge can of worms and you don't want to go there. Just know that you can't use the flexplate from the newer engine on your 68 289. The balance is different, changed from 28oz imbalance weights to 50 oz in 1981. You can use the trans fine, but make sure you have the correct flexplate for your engine to fit the AOD.