I did some more testing this evening and it led to more very interesting discoveries and positive solutions I think. First I just want to thank the LORD for giving me the wisdom to figure this very daunting problem out on my layout and I also want to thank all of you on this forum for all of the expert advice and information that led me to a probable solution. I hope my experiences will help someone else.
I will preface this by saying I believe the problem was caused by my wiring as GunrunnerJohn had speculated. There were 2 different aspects of the wiring that came into play here I believe.
From my last post you will remember that I had narrowed the problem down to the Fixed input channel 2 on the TIU.
First, I had my Legacy Base mounted on my control table between my 2 Z4000 transformers. The power wire for the legacy base as well as the power wire in the split PD9/Serial Cable/Power for the SER 2 ran very close to and in some instances in the same bundle of wires as the cables going from the transformer outputs to the TIU inputs. The wires coming out of the transformer going to Fixed input 2 were closest to these Legacy power cables.
Second, I had all of my transformer common's hooked together (2 Z4000's and 4 Z1000's) as stated by Barry in his DCS book. I ran a wire across my control table top from one Z4000 common to the other Z4000 common and this wire passed underneath and very close to all the wires coming out of the Legacy base. Additionally I had a common wire connected to 1 of the Z4000's from all of the common's on my Z1000's tied together. This wire passed very close almost touching the wires from the transformer to Fixed Input 2 of the TIU.
Third, I had my WIU on the control table in close proximity to the Legacy Base and the transformers and all the associated wiring as well. I moved the WIU to under the layout next to the TIU.
When I removed the Legacy cables from close proximity to the cabling going from the transformer to the TIU and when I removed the wires connecting the transformer common's together the DCS signal improved to consistently getting between 7 to 10 with a PS2 engine where as before it was anywhere from 1 to 6. Additionally, I then physically moved the Legacy Base to the floor a couple feet away from the control table and made sure all of the Legacy wires weren't close to the transformer to TIU wires. This gave me a consistent 9 to 10 DCS signal with a PS2 engine on the track connected to Fixed Input 2 and a consistent 10 DCS signal with a PS3 engine.
So, it appears that this combination of wiring routes and component placement was causing my issue. I can't explain electrically what actually was happening (there are probably many on this forum that can) but I know the changes I made solved my DCS signal issues.
Now, I will have to figure out the best way to rerun my wires that will yield the same results as what I am getting with everything "loose".
Thanks again for all the help in solving this issue. I hope this information will help someone else from having similar problems!
Michael