"The important thing seems to be , you want a tight fit in the tail section to hold the rod up in the middle of the bait."
Yes, that would be ideal if you want a perfectly centered core shot but I really don't think that matters ( a perfectly centered core shot ) with the larger baits. That being said, It may be an issue with smaller crappie sized baits. I am curious to see how thin a core hole a guy can get away with on the smaller baits.
"I'm sure that different molds will take different size rods"
I had to do some grinding on the pins to make them fit well enough to let the plastic flow on two of the three molds I tried the E core method with. In my case , I used 1/8" brass rod but I think you could go with a larger diameter rod if you wanted a larger core. You would have to pay close attention on how you ground the ends of those pins if you wanted a perfectly centered core color but it wouldn't take much ( less precise )grinding if you can settle for good enough centering of your core color.
I am enjoying figuring this process out .... so far. LOL