Bolt / clamp / whatever some sacrificial material to the bed at the locations you'll indicate off of to tram your head. Face the tops of those pieces using the router. Tram your spindle. Maybe resurface the locations you trammed at now that your spindle is straighter and recheck the tram. I typically have a MDF spoilboard on my router. I'll surface it with a bit that's not too large, maybe 0.5" diameter, then tram off of a 123 block that spans any ridges left by the out of tram spindle.
CNC mill build thread: http://www.cnczone.com/forums/vertical_mill_lathe_project_log/110305-gantry_mill.html