Decided to wire-wheel my transaxle today which is not installed.. the rear part of the shift rod is still attached to it though (just as I bought it).

My first issue is that the shift rod is stuck in the steel 'cup piece' at the transaxle. There doesn't seem to be a set screw that's holding the rod in place (is it possible to be so deep in there that it seems to be gone? I doubt that, but..). Anyway, I lubed all the pieces up w/WD40 and used a 3lb hammer and a drift punch to try and move the rod from the rear, it didn't budge. I didn't get too violent with it as I didn't want to mess up the rod that goes into the case. Any trick to this?

Also, the side shift console itself is loose slightly.. so maybe someone before me decided to try and get the whole thing off instead of just the rod, and didn't tighten it all bak up? Is this a method that might help without damaging internals?

Make absolutely there is no cone screw in there otherwise you're fighting a losing battle. Yes, it's possible it could be deep in there. Someone may have used a generic allen head set screw and it could be well below the surface of the cup.

Generally speaking when things are stuck and gentle persuasion doesn't work, the heat wrench is you next best friend. Wrap a wet cloth around the shift rod and the trans gear selector. This will keep it from getting hot (beyond 212F). Then heat the cup. I'm not talking red hot, just a gentle heating. It will expand the shaft bore.

Then try tapping things again with a brass drift. The brass drift helps ensure you don't deform the shift rod effectively swaging the road in place.

In this case you may end up melting the plastic bushing but sometimes you have to lose a battle to win the war. But be careful not to melt the transmission side selector seal!

Also use penetrating oil. Liquid wrench, PB Blaster . . . whatever. WD-40 is not very effective at penetrating into rust and helping loosen stuck parts.