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Any suggestions on how to keep glue out of the truss rod channel while I repair this crack?

If its a single acting rod which it looks like, unscrew and remove the adjuster nut. Coat the threads with grease or vaseline or wax. Maybe wrap some waxed paper around them. Since the rod doesn't turn and is under tension it shouldn't matter if a little glue gets in there but try to minimize it.

If its a double acting rod then you need to be careful - it does turn and you won't be able to get the adjuster off. I would still try to work some grease in around it with a probe of some kind - maybe a cut off guitar string. Make access to the nut thru your caul and after you've done the glue up reach inside and turn it every every now and then.

If its a double acting rod I would want it neutral while doing the glue up just like a new install. Otherwise it is pushing down below the nut and fighting your clamps.

As a strange aside, this truss rod nut sits proud of the neck, the nut needs a notch in the bottom to accommodate the rod. I've never seen that before...

Probably just a lot of curve in the channel

I sometimes wrap a short piece of a large plastic drinking straw like from Sonic or Arbys, slit down it's length.

What guitar is this?

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"Act your age, not your shoe size" - Prince

Its a Hagstrom Swede, one of the reissues...

A pipe cleaner liberally coated with Megiuar's car wax can be shoved down the channel and slid around to coat the surfaces. I've used this method on all of my headstock repairs and never had a problem.

Curiouser and curiouser...

I sold these years ago and now I remember Hagstrom bragging at the time about their H-expander or I-Beam truss rod. It looks like its basically a rail in the channel instead of a rod.