Typical overhead height for tunnels/bridges (O scale) - Model Railroader Magazine

Your highest piece of equipment, whether locomotive, rolling stock, or open cars that could carry loads making them higher than the aforementioned will determine the clearance height needed.
Obviously, if your track is on roadbed, rather than directly atop the layout's surface, you'll have to include that (plus the height of the track itself). 

I've seen this same question asked about HO scale, but seen to recall that most answers recommended clearances much higher than what I would consider adequate - I have the same issues as you with grades, but also model the late '30s, and a lot of current day equipment is much higher than what would have been common in the '30s.

Also, I deliberately made some overhead clearances too low, in order to add some operation challenges.  This means some cars or locomotives are restricted to certain routes, and the restriction also involves some regular moves involving excess height lading.  I also, for the same reason, included restrictions for excess width equipment - mostly MoW stuff, and a couple of locomotives. 

Since I'm a solo operator, there's nobody else to blame if I make a routing mistake, but such restrictions on a club layout, or a home layout which can accommodate multiple operators, could prove very troublesome.

Wayne