Last year I had a couple issues with my 06. First was a dying alternator which causes a slew of problems when the trans doesn't get proper voltage.
The next issue I was having was very similar to what you are experiencing. I chased a bunch of hypothesizes like trim valves, harness issues, leaky harness connector coming out of the trans. The actual problem was a mashed trim valve spring on my transgo shift kit. At some point the spring got hung up on the valve body and the valve proceeded to turn the spring into small pieces.
Symptoms were violent shifts, limp mode locked in gear, incorrect shaft speed codes.
Pull your A trim and B trim solenoids, the valve trims should pop out with the solenoid.
Best of luck.

Using screws and a lot of wood glue, the base was assembled and allowed to dry overnight on a flat surface

Don,
Great job on the cabinet construction. I use the Kreg pocket jig for cabinet construction personally and also we use it professionally where I work. The biggest benefit of them is the ability to glue up without clamps and continue to work through the drying process.  As a standard practice I do try to keep my fasteners wider and towards the edges of the boards. This tends to help with getting a tighter joint and holding the surfaces flush with each other while the glue is setting.
I'm curious about your decision to use wood drawer slides instead of HD ball bearing full extension slides. I would imagine these drawers will be weighty once full of contents and could prove more difficult to operate. The wood slides are certainly less expensive. Butchers wax is also another good alternative to use on the slides to keep them working smoothly.

I have 2 daughters 5 and 7 years old. 

Short back story.  October 2016 we decided we were done with debt and started an aggressive payoff or debt snowball.  My wife was worried about how we were going to do Christmas on a tight budget.  I think we spent $100 on each of our daughters that year.  Only 4-5 gifts each, which had us questioning how Christmas was going to be received by our children.  Christmas morning after all the presents were opened our children ran to us and said "This is the best Christmas ever!"  What a blessing that was and reassurance that we are doing the right thing. 

This will be our 3rd and last Christmas on our debt snowball.  The girls are getting a new bicycle, a couple small toys and clothing.