Finalizing on layout-suggestion welcome

So, the upper level is only about 5.5 inches above the lower loops?  Is that going to be enough clearance? 

I'm working on a track plan that I'm figuring I'll need around 7.5" clearance due to the cantilevers on my GG1, unless the GG1 is restricted to loops without overpasses....   hmmmmmmmm......

Due to the size constraints of the table, to get to 5.7" above the other track, I am at a 2.6% grade. If I raise that up more then I increase the grade. Some of my engines have traction tires but some of the older ones don't. From what I have read on this forum, I should try to keep the grade about 2.5%???

Personally, I would ditch the elevated return loop. The clearance issues combined with it getting in the way of the operating accessories makes it more trouble than it's worth. I had a similar loop on my 5x10 layout and eventually took it down. 

I understand what you mean about size constraints, all too well.  My layout is 18'x19' L, right now I have a horrible 4% grade to get up to 7.5" above ground level, the only two engines I've tested on it are my Lionel 2truck Shay which is heavy enough that it had no problem, plus I think its geared low, and also my Williams B&O F unit, which makes it up pulling a pretty decent consist of maybe 15 cars?  The couplers one some of the older cars were failing and I had to shorten it because of the weight. 

That being said, the grade is way too steep and I can cut it in half if need be by extending it along two walls.  Now, enough of my issues, back to yours: The point is you could probably get away with increasing the grade a tad, or just do away with the grade altogether.  I don't think 5.5" is going to be high enough when you factor in the roadbed lifting your bottom track, plus the subroadbed for your overpass, that may end up diminishing your clearance by almost an inch if you stick to the same grade!  Cutting it close. 

So, instead of a grade, consider and independent raised loop.  Now I know how you probably feel, I'm dead-set on having a hill to climb and ain't nuthin' gonna stop me!  Except perhaps physics.  Anyhow I just don't think that your height right now is going to be quite high enough. 

Another thought, would it be possible to move the crossover switches to the other side of the layout to free up that length of straight track on the inside loop before the beginning of the grade?  That looks like it would give you an extra 4 feet of straight run to add onto your climb, which at 2.5% would get you to 6.9" above the table, much better for clearance.  I'm guessing from reverse calculating your height and grade that right now you have about 19' of climb, that extra 4 feet would make a bit of difference. 

In fact, if you increase the grade slightly to 3% with that total length of about 23 feet of climb you would get up to just over 8" above the table, much better clearance.  Now I don't know how all your locos will behave, I personally set up some test tracks at different grades to see how mine would do.  It seems to me that for the most part the "2.5%" is pushed based on the desire for a gentle, prototypical look.  If that's not as important and you're more concerned with just getting those darn trains up that hill, then a steeper climb is possible.  In fact, I've seen plenty of layout photos with grades that can't possibly be near 2.5%.  Like I said, my little guys will get up that 4%, it may take full power from the transformer, but they get up it! Personally I'm going to lower that to at most 3.5%, hopefully lower.