I guess I'm posting this mostly as a tip for others, as I *think* I've now landed on the proper bolts for my situation.
I recently ordered a new timing cover for my 65 289, and the closest match to what I had on there (which was a C50E-6059-A1) was this one: https://www.summitracing.com/parts/SDK-C5AZ-6754-A (C4AZ-6019-B). They seem identical in all aspects, except the lower bolt holes are all thicker (requiring 2" bolts) whereas the old one had three lowers that were thin and only one requiring a 2" bolt. So the AMK bolt kit I had ordered (AMK F-489 Mustang Timing Chain Cover Bolt Set 289 1965-1967) doesn't work, as it comes with 5 short and one long bolt. I ordered extra long bolts from Amazon -- I guess I'll have a few extras: https://www.amazon.com/dp/B006HY8PZK/ref=biss_dp_t_asn.
I recently ordered a new timing cover for my 65 289, and the closest match to what I had on there (which was a C50E-6059-A1) was this one: https://www.summitracing.com/parts/SDK-C5AZ-6754-A (C4AZ-6019-B). They seem identical in all aspects, except the lower bolt holes are all thicker (requiring 2" bolts) whereas the old one had three lowers that were thin and only one requiring a 2" bolt. So the AMK bolt kit I had ordered (AMK F-489 Mustang Timing Chain Cover Bolt Set 289 1965-1967) doesn't work, as it comes with 5 short and one long bolt. I ordered extra long bolts from Amazon -- I guess I'll have a few extras: https://www.amazon.com/dp/B006HY8PZK/ref=biss_dp_t_asn.