Has the bellhousing been indicated in to concentricity with the crankshaft? Have the engagement teeth on 3rd gear and the internal splines on the slider been checked for rounding/wear/damage? I'd start by pulling the side cover and inspecting the teeth, that's the easiest.
You may be on to something with the bellhousing. Years ago when we assembled the car, I dialed in the bellhousing with the new motor and we installed a used Muncie behind it. When measuring for the driveshaft we discovered the output shaft splines were twisted and in a rush to get the car together for Drag Weekend we stole the Muncie from his Corvette to use (worked fine). Long story short, shortly after returning from Drag Weekend he ended up pulling the clutch and the transmission back out of the car to swap in a new clutch and the previously removed damaged Muncie which he had since rebuilt. From that day forward, it's always kicked out of 3rd gear. He did make a comment about the shim stock I had put between the block and scatter sheild and I'm wondering if maybe they didn't go back as previously installed.
As I recall, the sliders and internal splines looked good when he had it apart but I can't speak to that with certainty at this point as its been quite some time. Certainly worth looking into though.
As much as I hate to do it, it's sounding like that transmission should probably come out to check that scatter sheild again. Could it really be that far out to cause this? Would it not affect any of the other gears?
