The TR3 MC is a lot simpler than the later cars, it's hard to have much wrong with it. Do you get more air when you re-bleed the brakes? Have you checked the soft lines, rear brake adjustment, no stuck caliper pistons, etc?
Not sure I understand your comment about the pushrod. The "car connection" is just the top of the pedal, which should move easily. IOW there is no need to disconnect it. In fact, that's a good point, the pedal needs to return fully and easily. If it binds due to rust in the pivot or whatever, and doesn't let the MC return that last little bit, you'll have problems. There also needs to be some free play at the pivot. Not usually a problem with the later cars, unless perhaps someone has added a pedal stop. (Earlier TR3/A came with a pedal stop from the factory, but it was deleted later on.)
Also, the residual pressure valve on top of the 5-way connector can sometimes cause problems if it gets gunked up inside. If all else fails, you might try cleaning it. Or just leave the plunger out entirely as I do. It's actually supposed to help prevent a low pedal after hard cornering, but I would rather deal with the low pedal than have the brakes drag a bit all the time.