Does anyone know if a Alpha drive will work with a MC1 drive coupler?

It should, I beleive the input shaft splines are the same.

we installed an older motor that had a MC1 drive and had to use the coupler that was with it. When we tried to install the drive the input shaft dosn't want to slide in, we checked the alignment and it's good...any ideas

when you checked the alignment, was it with a alignment bar.
as far as I know the spines are the same. maybe someone else has some input?