The afore-mentioned are probably your best bets. My experience with mating an 3 speed OD trans into a chevy 348 on my 1957 pickup was exactly the same. I couldn't get the trans in the last 1/2 - 3/4 inch. In my case I found out that there was a short throwout bearing and a long one (if I remember correctly the stock one was the long one). The differentiating factor was that my clutch was a competiton clutch and pressure plate, not stock. The short throwout bearing solved it. If nothing else works, it is something else to investigate.
don
