^^ Yes when you install any of those mounts, you should tighten the mount together with the engine before you tighten it to the body. Like on the transmission side: jack the trans until the mount is floating about 1/8" above the bracket that the mount bolts to. Now bolt it down, and get it as snug as possible. What you don't want to end up doing is pulling the center stud up with the nut- lifting the transmission with the mount. The trans should hang on the mount, but not be lifted by it.
Other than that, yes, improper engine alignment on the mounts will cause some vibrations.
I'll check my Helms and see what the procedure is for lining the engine up in the engine compartment. I marked the location of my mounts before removing. I changed all mine out to poly mounts, but I don't mind a little vibration at idle. It's really not that bad. It's a whole lot less than it was with bad mounts.
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