is correct in that the 400CI would be easier with regards to part sourcing, but with all thw aftermarket availability of custom pieces, you could do a nice rebuild on the 389CI.
Reading your post, I assume you have fabrication skills, and may like a challenge.
Your first hurtle will be that the starter bolts to the bellhousing, and not the engine block. So you would have to use a matching bell. However, you can purchase an adapter that would solve this problem. It allows for a later 1965 Chevy/BOP and up bolt pattern bell transmission. Has provisions for a starter mount as well. It is for an automatic trans, but my guess is if you were to contact the company, they may be able to let you know if they offer a kit for a manual transmission. Wilcap Pontiac Engine Adapter Page
Engine mounts are most likely different, so a little fabrication may be at hand. Possibly grafting the cradle mounts from the GP over to the '64?
Transmission crossmember might need some attention, but with all the aftermarket tube style trans mounts, this would be easy enough to get to work if you could not modify what you already have.
The 389CI would be more "period" correct and you don't see these used as much anymore with the 400CI or a stroker slapped in in its place. Butler has stroker kits which I am sure you are aware of.
Heads can be used if no cracks, but I believe you will find that the oiling for the rockers goes through the engine/rocker arm studs. They are also 3/8". The SD engines used a 7/16" stud and it was pinned, not a screw-in affair. There is a replacement 7/16" stud that is offered on Ebay designed for the early heads. As he states, insert these and then go with pushrods that have the oil hole in them to oil the rocker arms. He has sold a number of sets and has a 100% positive rating. Check this option out: https://www.ebay.com/itm/Pontiac-GTO...UAAOxy7MtRuncH
I assume the valves are the smaller 1.88" Intake/1.60" Ex.. The HP 1964 and up 389CI was 1.92"/1.66" and the SD head used 2.02"/1.76" valves. You can size the smaller valves up. One trick is to use the Chevy 283" 1.94 Intake. Same length and dia as the Pontiac. It has a double groove keeper, so this is where I don't know if you can use the Pontiac spring retainer/keepers or have to go with a Chevy match. The thing that will limit the Intake size is the closeness of the Int/Ex valves in the center. Another former member did this and I cannot recall what intakes size he went up to, but did say you were limited as to how big you could go in diameter. It may have even been the 1.94/1.66 combo.
A good gasket port match and blending in the bowl area if going with the larger valves will help. I like bronze valve guides & Viton valve seals if you can use them. Keep the 1.5 rocker arm ratio.
Intake for me would have to be a tripower. You will have to get one to match your intake pattern on the heads. The 1964 GTO and 1965 & up Pontiac uses a different pattern. The intakes can sometimes be cheaper as they are not in big demand. Check this out: https://winstonsalem.craigslist.org/...879896408.html
You can go from there on cam choice and other goodies. You will use all the pulleys/water pump cover, balancer, etc. from the '63 engine.
I am no expert on the earlier engines, so I may be missing a few things. You will have to do the research. I don't know if it'll cost any more to rebuild the 389 vs a 400 as I don't see a lot of difference when it comes to same machine shop needs and parts. But, would look nice with the 389 valve covers and tripower under the hood if you can make it work.