Alignment issues: If the transmission mount is not lining up, loosen your engine mounts. If your installing an engine first, do not tighten the engine mounts before installing your transmission. There is a lot of wiggle room at the engine mounts, if they do get tightened first, you can have alignment issues at the transmission mount. It’s more critical with solid engine mounts.
Transmission Mounts: Always install a rubber or polyethylene transmission mount. NEVER install a solid transmission mount!!! Trucks frames/chassis do flex. With a solid transmission mount, as the truck flexes, your engine/trans does not and it will find the weakest link and that is your bellhousing.