Sometimes, what you did is what you need to do to get that transmission to seat, as long as you tighten the bolts slowly & on the diagonal. If ANY resistance is felt, STOP. Be sure to double check everything next time before the transmission goes in, don't take someone's word for it, they could be wrong. Those things are HEAVY, especially doing it on your back.
P.S. Make sure the clutch alignment tool (Splined like your input shaft & usually supplied with the new clutch kit) slides in & out of the installed clutch easily to be sure the clutch disc is perfectly lined up. That helps a lot too.