Todd,
If you had a GM Big Block in it before monted with a stock type of mount, then the Merlin should be exactly the same mounting.
If you had a GM Small Block in it, that is the difference. GM Frame mounts for the Big Block and the Small block are different.
What kind of car and what kind of mounts were working with what kind of engine?
As was said at times you have to struggle some to get things to line up right. Loosening motor mounts to the frame helps at times. Raising the car higher so the engine can tilt more when going in helps at times if you are installing with tranny.
There are more than one type of motor mounts that look the same too.
Check your new motor mount part number and see if they are for correct engine. Check to be sure that motor mount will match with your frame mounts.
Ed