mx-6 halfshaft

my friend just swapped his automatic transmission to a manual transmission. he has a 96 mx-6. he got the tranny from a probe in a junk yard. the problem is that the halfshaft is not lining up, does anyone know what could be wrong? and what we can do to fix it?

okay i just recently had the same problem so what i did was look up to see if the halfshaft for the manual transmission was diffrent than the automatic well the halfshaft is the same but the jack shaft which is the inner piece of the halfshaft is different on the automatic it is shorter but this part was hard for me to get so what i did was go down to the autowreaking yard and ask them to find me the jackshaft and they found one for me with in a week. but that is all u have to do.