Motor mount alignment

I had some engine vibration so I checked my mounts and sure enough they were bad. I replaced them with some made by anchor. After the end tall there is still some vibration that can only be felt between 1500 and 2000 RPM. I don't really feel it when I'm driving untill the revs come down when coming to a stop. A mechanic told me that the mounts were not sitting in there properly and some of the vibration way be due to the aftermarcket mounts instead of factory. My question is, how do you properly line up the engine and mounts? Has anyone else used the aftermarket mounts and had this problem?
 
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In that picture trombonedemon posted, do you see the little bump on the motor mount that is about 2 inches to the right of the long stud? Assuming I remember correctly, that little bump sits inside a hole in the K-member. There should be no adjustment in the alignment of the motor mounts, or at least very little.
 
I see the bump your talking about. Guess I need to make sure that bump is in the hole. Thank you. Has anyone used motor mounts from a local parts store? Anyone have any vibration with after market stock replacement mounts?
 
Well I looked at the mounts again and they seem to e right where they should be. They don't allow the engine to move much though so I guess they are just a little stiffer than the stock mounts. I'll have to get some new ones from ford. Thanks for the help.