Kevin, we had 27 here today for our early Easter celebration, so I haven't had time to enter your dimensions. Tomorrow I have to finish taxes and pack, so I don't know if I'll get to it before we leave. If I don't, I won't get to it until Friday.
Getting them down to 2% is going to be impossible with the current design. The length of the bridge to the nearest turnout decides how steep the grade it. The only way to reduce it is to lower the bridge or move the turnout further way. FWIW, I played it safe. The yard is at 0", the TT and Black tracks are at 12" and the bridge is at 19". The bridge can probably be lowered, so I lowered it to 18" (6" clearance) and the grades to/from went to 3% or less.
Now, you can lower the other tracks too in order to reduce the grade to/from the yard, but that will reduce your ability to deal with problems. Even 12" is limited by whatever you use for framing beneath the sub-roadbed. I have no idea what kind of benchwork you intend to build, so I can only take the software so far. There are still a lot of unknowns that have to be determined before any design can be finalized. If it weren't for the hidden yard, things would be closer to being done, but you need to decide on benchwork and how much space you want for access to the yard. If you raise the yard to only 10" below grade, that will lessen the grade. If you shorten the yard, that will lessen the grade. Do you need that much storage space or are you just filling the space is a question you need to answer. You can have the yard 6" below grade, but then you'll have a very hard time getting your hands in there. 
To show you what I've gone through to keep things straight for the layout I'll be starting next month, here's what I put together to show the various elevations. And I still need to update it because I've decided to change a few things.
