How do you line up the engine mounts and trans crossmember on an LS swap when holes don't line up?

Make one end adjustable and set the other where it needs to be.

• Engine side: Adapter plates bolt to the LS block and take a classic small-block Chevy 3-bolt mount; different hole positions move the engine fore and aft. Flat adapters like ICT's give several mount positions and raise the crank centerline slightly (0.177 in in ICT's case — note it if hood clearance is tight). Adjustable mounts use carriage bolts in slotted plates, so you can slide the engine fore and aft, then lock it down. Speedway's writer used them to dial the engine position exactly after changing headers and dropping a supercharger that had needed the engine 1-1/4 in forward.
• Transmission side: adjustable swap crossmembers have slotted holes and use the frame's multiple factory holes for fore/aft adjustment. Some also offer multiple heights to set the driveline angle.
• Order of work: set the engine position first (firewall, header and hood clearance), then locate the crossmember under the transmission, then measure for the driveshaft.

LS mount bosses are roughly where SBC mounts were; common adapters convert the LS block to the classic three-bolt Chevy mount; adapter hole offsets move the engine fore/aft.