Did you follow the book to the letter when you rebuilt it? Make sure everything went back where it belongs in the correct direction? There's a LOT of itty bitty pieces in those things and one wrong move will booger something.
My first thoughts on a transmission that won't shift properly actually are related to the clutch and pilot bearing. If the input shaft is under load it's not going to shift properly. Second thought relates to the detent balls and springs on the rails... or bent forks.... or bent rails.
Bearing preload could also be a factor. Any time you change a bearing you're going to need to reshim... or at least check that the preload is within spec...