gearbox install advice

hey guys i just installed my 4 speed box to my 68 383. the engine is on a crattle on the floor. i installed a new pilot bushing and a new mcleod clutch and TO bearing and had the fly wheel resurfaced. my problem is i had a hell of time getting the box to line up. i used a alignment tool. i once put the box in under the car and i had less problems then tonight on the floor. i had to pull the last 3/4 " together wiht the bolts. but it slid together good. is this normal when you are using new parts like i did? thanks