Rontierra, as you said "It's hard to trace through that board"
I spent hours reverse engineering the board and decided to post it to be nice. Out of all that work I only see one omission, The 10K pullup resistor for Q3 is missing. Any one with a brain could easily see what that part of the circuit is doing even with the resistor missing. I wasn't designing the board I was reverse engineering it to get an idea of it's capabilities as it obviously had more than the manufacturers "datasheet" suggests.
In the two problems you state you made an OBVIOUS ERROR (to use your words) on one. You stated "Q output of the CD4541 shows connected to Vcc (shorting the output)". Q/nQ select (pin 9) is an INPUT to select the default state of the output (Q) on pin 8. Connecting it to VCC makes Q high after reset.
So after 1300+ downloads not one person has said thanks. All I see are whiners who want everything handed to them so they don't have to think or learn and now an inconsiderate person who overstates a problem on the board and makes a real obvious error not even getting his criticism right.
I wish I could pull the schematic I posted off. I have a newer version of the schematic with the pullup resistor added and also directions on how all the inputs and outputs work. I don't think I will be posting it any time soon.