Perhaps I’m confused also, but where did you get 5.5" from? Are you trying to tram your machine using a square held against the router body? It might be worth making a traming beam and using a plate of glass so you know you’re adjusting to the motor axis, which may not be true to the router body. You can essentially get it to withing thousandths in any direction within the limits of your plate of glass, which tends to be dead flat. YouTube has some good instructions for doing this with other machines and you can adapt to using those techniques with the Longmill. You could also buy a tramming gauge set for about $100. Might need it once a year if that but if you want near perfect accuracy that’s the way to get it. I see tramming like I see guitar playing… we spend half our time tuning our guitars and the other half of the time playing out of tune. You will never achieve absolute perfection but have to figure out where your happy medium is.
You can also get some of the tram out if you loosen the gantry to side plate screws and twist the gantry forward or back and retighten.