You may have the "worn dogs" issue on the C2-C5 gearset. Also, the pre-K4 engines had a shift drum that tended to wear on the nub that pushes the fork back & forth between 1-2 gears, which then makes it real stiff. When this happens, sometimes the screw on the end of the shift drum comes loose from the effort, which can lead to bigger troubles like a bent fork, later.
If you rebuilt the engine, a few questions:
1. Did you also install new O-rings at: the countershaft bearing oil feed to the tranny, the 3 that seal the oil pump to the bottom of the engine, and the 2 that seal the oil hose to the side of the engine? These all need replacement by now, and will 'suck air' or leak pressure if they are old and shrunk. If you split the cases, also replace the 18x3 O-rings at the front oil journal and the Neutral Switch.
2. What kind of oil are you using? If you use the [in]famous "V-Twin Motorcycle Oils" out there, they will almost lock your gearbox like it has sand in it. They have WAY too much detergent in them for these bikes: use a low-detergent, 20w50 or 15w50 oil only in the Big Four.