I did find the short last night. The issue was with an Atlas Snap Switch in which the rails on the frog ended up touching. Maybe because of soldering joints? I am not sure. We have replaced the switch and all is well except for now putting every thing all back together. Thanks to everyone for their ideas and help to resolve this problem.
We also received two packages in the mail today. One was from Walthers, which included two new projects, a GP40 that is painted Western Maryland and my goal is to create a Tacoma Rail GP40. The package also included the Rusty Rails kit for painting rails that we will be reviewing, so stay tuned for that. We are also excited that we received a package from Bragdon Enterprises including their Weathering system. This, as with many things, is the first try at weathering so we will be sharing our trials and reviews of this product as well.