3rd Gear

[larrys40]

As Tom indicated realize that the throw to 3rd is shorter than 1st or 2nd, as it is just moving the second/high slider forward to engage with the main input shaft splines.
My guess is that the problem is in the shift tower ( forks worn/bent, springs/detent worn) or shift lever. The ball must be trued round and fit properly within the fork assembly.
Just because you swapped assemblies doesn't mean that they both couldn't have issues.

I doubt your pilot is bad..... I would check all of the above first, If you hear noise from the pilot you can always pull the rear back, remove the u-joint and rear trans retainer and sliders along with main drive gear shaft out the back of the trans, and depress clutch and spin input shaft and feel for roughness/fore/aft movement. If the bearing retainer were on wront it would probably be making a scraping noise.....

Let us know what you find.
Thanks,
Larry Shepard