This obviously won't be a super constructive comment, but I have consistently advocated for pressure bleeding vs vacuum bleeding. I'm not 100% sure this is the issue you're experiencing, but at least on my Goblin, the lines between the reservoir and the clutch and brake masters will leak air into the system when vacuum bleeding, but do not leak brake fluid out with pressure bleeding.
Because I got air pulled into the system when vacuum bleeding, I can't say how effective vacuum bleeding would have been on the clutch slave cylinder. But I can say, with pressure bleeding, because the clutch slave cylinder is after the clutch bleed valve (what you're calling a zerk), a clutch bleeding tool can't get the air out of the slave cylinder.
Whether using a pressure bleeder or using no bleeding tool at all, getting the air out of the slave cylinder requires pressing and holding the clutch pedal (pressurizing the system and the slave cylinder), opening the bleeder (zerk), allowing the slave cylinder to decompress and push air/fluid out of the bleeder, closing the bleeder, and releasing the pedal. Also note that due to the length and horizontal orientation of the line running through the tunnel to the slave cylinder, raising the rear of the car can help get air bubbles to and out of the bleeder.
I'm not sure your issue lies with bleeding, but figured I'd lay out some of my thoughts to see if that can jog any inspiration on your end for potential clutch hydraulic issues.
Back towards productivity, if you got the chance to drive it, did the trans shift well when it was still in the Cobalt?