I forgot to mention something about tramming. Tram front to back first! For front to back, you need to shim behind the top or bottom of the tramming plate, (or behind the top or bottom of the router mount), depending on the direction indicated by the dial indicator. I went with, and recommend, shimming the tramming plate. Also, I used standard weight aluminum foil for shims. It's .0005" thick, half the thickness of my thinnest steel shim stock. Anyway, If you don't do fore and aft first, you risk messing up the right to left tram when you loosen the tram plate bolts. Less risk associated with front to back first.
I used plate glass for tramming, but only after I was satisfied my spoilboard surface was parallel with the gantry. I started out trying to shim the glass, but found that the slightest pressure on the glass would cause deflection, and sheets of paper, business cards and the like were too irregular to reliably use them. Also, the glass wanted to slide around and scatter shims when I tried to insert new oI found myself trying to chase shimmed flatness for a couple of hours before I figured out I wasn't going to get it. Then it hit me that even with slight ridges from out-of-tram surfacing, the plate glass would ride on top of the ridges evenly. All I had to do was ensure that the glass was clean and the spoilboard was free of dust - so the glass would lay flat. Sure. it's possible that there were small irregularities in the glass, but decided that the cost of marginally greater precision (precision ground granite slab) wasn't worth the cost and effort. Besides, MDF isn't ever going to be precision flat.
I stayed with the plate glass, because I couldn't rely on my dial indicator plunger to read consistently from either a ridge or a valley. Like David, I have a flat round plunger tip. I use mine to set jointer blades. However, with glass, I wanted the accuracy I thought (perhaps wrongly) a more pointed end would give. At the end of the day, my results were both acceptable (within .0005") and repeatable. (Note: .0005 is not entirely certain, because not all of my measuring devices are certified or even advertised accurate to that resolution.)
Gary