While I can't really offer you a specific remedy, I can tell you that you are not alone!
The exact same problem happend to me after installing a dual disc clutch in January of last year. I fought it until this June, when the clutch started slipping (prematurely). I pulled the clutch and returned in to SouthBend at Peter's request. He sent me a new one. But there was no discussion or consideration as to why the transmission was difficult to shift. Only that it wore out early. In any case, while the transmission was out I had it rebuilt by some local guys, which included new bearings and syncros. Since then, it shifts much easier now. Not like it did before all this, but much better. So I can't say whether the rebuild or the new clutch made the difference, or it was a combination.
During the time of the problem, everyone suggested it was a tight or mis-aligned pilot bearing which was causing the input shaft to continue to spin a little. But when I pulled the clutch in June, the bearing was smooth and square in the flwywheel. No indication of a problem there.
So it may be that the only solution is to pull the transmission and clutch again. Check the pilot bearing, and maybe consider having the transmission rebuilt, depending on the mileage. Mine had about 125K on it. The problem never got any worse or any better during the time the original dual disc clutch was in. I really got to hating my 5 speed during that time.
-Jay