Well, you can buy rifle barrels for Type 99 Arisaka rifles on GunBroker form people who have taken them apart to sell the parts. You can buy barrels and barreled actions. My understanding is that it is impossible from a practical standpoint to re-barrel one of these rifles even if you have the spare barrel off of some other T99 rifle (e.g., by buying one on GunBroker, etc).
If you want accuracy, your .312 bullets will likely be more accurate than the .308 bullets, but as someone else said above, sometimes the .308s will work fine in individual T99 rifles and you just have to try it. Good work getting the bullets and brass. For powders, I use I-4064 and I-4895 and they work great. 3031 is problematic, partic in cold weather and with brass that is not once-fired in that chamber. I'd avoid 3031 unless you can not find any other powder. You can use H-335, though people say it is not as accurate. You can use the 4350's too. People say that 4064 acts like a slow powder in large cases/loads and acts like a faster powder in smaller cases/loads. It works great for the 7.7x58 Japanese.