As far as the over heating goes, first thing is to check the thermostat. Its probably not working and is stuck closed or barely opening.
Here's what I think might be wrong (done this myself) - You might have overfilled the radiator, up to the neck. And since there is no room for expansion the antifreeze gets hot and boils over. Since it is boiling out the neck it is not properly cooling the cylinder head or block.
As far as the thermostat working "congrats" on a working gauge! I don't think any of mine work, they are either stuck at the bottom or top. I think one might go from the bottom and pegs out at the top once at running temp, but I know it not overheating.
Other issues that might cause it to run hot, but not really overheat -
-Dirty/clog radiator - boil it out or from Greg get water hot and run some vinegar through the system
-Over filled radiator - anti-freeze should just cover the top of the cooling tubes - should NOT be filled all the way up to the neck of the radiator. The Nihon radiator is vertical and not the better designed horizontal/cross flow type radiator.
-Water pump going bad - should just leak out the weep hole and not really over heat - fan blade is turning right? if not...
-Belt tension - might be too loose and slipping or generator and/or water pump are going bad and not letting the belt turn...do you smell burning rubber?
-Anti-freeze it not diluted properly.
Okay, you probably know all of this, and again, the above might cause it to get hot, but not necessarily overheat. So if you are a GO and have no issue as listed above, I'm kind of at a loss. The E1 is a durable engine where oil and anti-freeze are optional.
I'm working on Shroom, '64, and getting the tool boxes ready to go get my '65 at my parents, so I'll be checking in. Just let me know if you any further issues.