1/8" hex head brass pipe plugs work great too. The threads match the metric 10x1.0 quite nicely and the taper binds them tight.

So far I just plugged the big hose which attached to the smog pump via the EGR.
The vacuum hose from the EGR to the throttle body is still in play so far.
My drop off at deceleration issues seems to have gotten worse. When I push in the clutch at or above 2000 rpm, the idles drops to 300 or so and then recovers.

I'll assume this apparent increased occurrence of my deceleration issue is not related to my removal of the smog pump?

I've removed my smog pump and EGR valve, and also the bracket for the smog pump. Good thing the bottom stud was short!

So, is there a reason from a performance stand point to remove the Christmas tree and then plug those holes?

Might be a good idea just because there is some rust developing.

Smog Pump Removal - Cam Housing to Cover Stud Replacement
 

So, after years of keeping my smog system in place (for no good reason), I removed the pump, diverter valve, air injection manifold and installed plugs in the exhaust ports. I'd like to replace the 2 top studs with shorter ones if I can with the engine in the car. I tried the double-nut, propane torch method to remove the studs, but I was concerned about snapping them as they weren't moving with pretty decent torque applied. Chances are I just didn't heat the studs enough?

Question: Can I remove the studs with the cam housing cover (and gasket) in place without damaging anything with more heat?

I just double nutted mine, then took them off without heat. I note that my heat exchanger bolts all came out without heat too.

Can’t comment with knowledge on heating the stud and effect on other things. Suspect it’s fine but no experience. Would be surprised if the mounting studs won’t come off double nutted with no more heat.