You might have to wiggle things around and jack up different points of the engine and/or attach different mounts in different orders to get everything to line up. Having all the mount bolts loose but engaged helps too.
Are all your rubber mounts in good shape?
Oh, also, it's important (for other reasons) to have the spacer between the engine and transmission. It is about 1/8" thick. Do you have that thing installed?
use the correct mount. the auto mount will require the use of longer tranny bolts and spacers. it will also cause the bolts to seize up in the lsd cover and then you will be replacing the cover. I know this because some butt hole did this to the 94 se-r I used to have and I had the displeasure of fixing it.