You need an absolute, rock bottom, don't-even-ask, 2.6" for 95% of what you are likely to run. That will let a Lionel Challenger pass below with no paint scraping up on the cab roof. Obviously that is too low, so I figure closer to 3" for looks, now that the safety part is determined.
But it is not quite so easy. Whatever the upper tracks must use for support/roadbed is going to have a thickness, or a height if you will. So, the 3" clearance above the lower rails must be to the bottom leading edge of that supporting complex, whether a girder bridge or the top of a large steel culvert. That means you must factor all this in to our grade calculation, and you may find that you need something closer to 3.5% for your grade after all. If that is a no-go, then you have options to alter your upper support compex, or even to have the lower tracks dip on a slight grade to that point, thus buying you some extra clearance at the bottom of the dip, after which it rises again to its previous level. Some fellas have to do that to keep their grades from getting out of hand.
I always use 3" as a bare min for clearance itself (3 1/4-1/2") allows breathing room. When working with railhead to railhead 4" is a general rule. Most bridges will only be no more than the 1" unless there are extremly thick/ tall girders. You need to adjust for for the bridge type.
If you find that you're grades create close clearance, using a short ballasted deck bridge built with 1/4 or 3/8 plywood. The track can be bonded to the ply and the the girders glued to the plywood sides. Remember if clearances are too close for comfort or you would like more clearance for a better or longer bridge, the lower track can always be dropped before the overpass.
On the club layout, I have the opposite problem. Many of all the track crossings are 5 1/2 - 6". This poses a problem with scenicing all my abutments as most ready made castings and molds are all 4" tall. Custom molds are made or other creative measures are needed in this case.
Modeling B&O- Chessie Bob K. www.ssmrc.org