My new Lee Pro 1000 manual says to use only CCI or Remington primers. I purchased primed .38 spl brass. Aside from disabling the primer punch out from the resizing die, what else would I have to disable? Thanks!

Lee lost a suit against someone using their hand primer that went off while priming. After testing they only advise using those two primers while priming cases.
With removing the decapping punch and leaving in the button that sizes the nose you are good to go.

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Front sight and squeeze

I have loaded tens of thousands of primed rounds, 9mm, .45acp and .38 special, on my pro 1000‘s with Federal and a Winchester primers using a two step process over the years without any issues.

I have two turrets for each caliber, one with just the deprime/sizing die installed. Fired cases, with a bit of spray lube, are run through the press with this turret in place before the cases are hand primed as I was loosing too many primers using the press system.

The second turret has the expansion/powder drop die in the first station and a factory crimp die in the third. Some presses have the priming button removed, other do not.

I also run my competition rounds (compared to practice rounds) through a press mounted priming die just to ensure they are seated correctly as my hand primer sometimes does not seat PPP’s properly.

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View from down under

I've hand primed for years and still use the press "as is" (never took the primer punch out). I put them in the press primed and have never had an issue...

Thanks everyone. I shall proceed.