408 Magnum stroker running hot.

I'm going to assume the pump is fine. I had an OEM pump on it and since replaced it with a high volume. There is water movement through the radiator looking in. Im not sure if its enough and I don't know how else to tell.
It's not about movement so much as it is about pressure. The system needs to build up 15lbs of pressure. A slow spinning WP may not build up the appropriate amount of pressure. This can lead to steam pockets and cavitation.

The timing is at 16° and 33°. I have a limiter plate in a factory electronic distributor. I've played around with the timing some to try and solve this issue.
i'm not an expert on timing. Hopefully someone else can confirm you have that part in order. While you are at it, make sure you don't have any vacuum leak issues as well.

I thought the 3 core would be enough for what I have. I plan on putting A/C back into the car eventually but the condenser and such has been removed for now. I put an overflow/puke tank on it to help with keeping the system filled.
normally it should be but you have a gremlin or your build just so happens to need more volume. Each motor rebuild ends up different. You might spend a lot of money and time chasing the gremlin or it's possible you could add more volume and the problem goes away.

I haven't thought about a head gasket issue. I have changed the oil once already and I check it often. Its not milky. The exhaust is clear and doesn't smell like coolant. Do you think combustion gases are leaking into the cooling system?
You can do a simple chemical test available in a parts store or online to confirm you don't have that issue. Good luck!

I answered each point above in the body of your reply.