This is just a wild guess, but while you had the transmission out, did you check the pilot bearing/bushing that's pressed into the crankshaft? Usually, this will give you more symptoms than you describe, like vibration when the clutch is depressed and the frequent need to replace the front transmission bearing. But it can cause the symptoms you describe... With the transmission shaft not perpendicular to the pressure plate, there is always a degree of contact between the clutch plate, the flywheel and the pressure plate, thus preventing a smooth shift or in severe cases, any shift at all.
The likelihood of this being the problem is somewhat remote, but if you have to pull the transmission again, it's certainly worth the time it would take to inspect it. While it's commonly called a pilot 'bearing,' it's almost always an oil impregnated bushing, kind of bronze colored and pressed into the flywheel with an interference fit. If it's loose, Loctite makes a compound made specifically for this problem... To fix bearings and other cylinders that are supposed to be an interference fit but for one reason or another have become a loose fit.