Need help with an engine swap!

I have an 87 D50 2.6 auto and am currently trying to swap my engine with another 2.6. While my new engine is a 2.6 from a D50, it came out of an 82 Ram 50. The problem I'm having is that my new engine doesn't line up with my tranny. i am sure that my engine is ment for an auto trans, but I believe that Dodge started using a different trans in 87 and not the 906 3speed which they used for years before. I was wondering if i could make my 82 2.6 engine fit my 4speed auto tranny in my 87 D50. I thought that the only thing that wouldn't line up would be the bottom two bolts and I was just planning to trill new holes for the bottom bolts but the shop says that the engine doesn't line up at all with the tranny I have in the truck. Please help!