I was finally able to mess a little more with the OTS last night. Based on the information in this forum related to the proper orientation to use when adjusting the OD Trimmer (should be looking from the input side of chassis towards the trany) mine came from factory set at 2 o'clock.   

I never messed with it because looking in the opposite direction it looked like it was at 10. I backed it off to about 10-11 and the low end issue I was having improved. It's still there but much more manageable than before. I tried to go a little lower but felt that 10-11 is where i like it best. I'm inclined not to change a thing with the cathode bypass cap but am curious about the frequency cut off detailed by bluesfendermanblues. I am going to lower one the caps a bit and see what happens...stay tuned...

Great...Thank you bluesfendermanblues! This is awesome information. I will definitely watch myself inside the amp...no doubt. At least you have cleared up some doubts as to what I was looking at in the layout which is extremely helpful.

For right now...I will take your advise and mess around with the settings before getting in there and changing stuff. I have definitely noticed the range of tones available by just adjusting the input, volume and OD gains. Reminds me of my MKIIc+....

Anyway...thanks again for all the advice.

And don't forget the "Patch Cord" mod which does some similar things and is not permanent. Just a 6foot to 2foot patch cord across the send/return jacks sending the signal through a 250pf cap and 220k resistor in parallel.

http://soundclick.com/share?songid=6575515

After testing with various length cords, it seems the cord length may have as much effect as the resistor/cap network.
That clip is with a particular 6ft cable that sounds good in the loop.

I was able to get in touch with Gil Ayan and he responded with the exact placement of his mod...heres are his comments in case anyone wants to know exactly where he placed the components in the circuit:

"The resistor and cap are in parallel to one another. Interrupt the connection between the wire that comes from the relay board and the 220K resistor at the input of the overdrive, and insert the pair (4.7M//.0047uF) in series with that. So, relay to 4.7M//.0047uF, to 220K resistor. "

After playing the amp for a few days, it seems that the problem still exists even messing with the OD trimmer. Because of this, I actually removed the trimmer and placed a 100K pot where the unused ground switch was and wired it accordingly. Now I can adjust it on the fly which has really helped in dialing it in. I also lowered one of the caps in the OD channel but still seems a little funky when playing single notes in the lower registers. Since I like tinkering with this stuff,  I'm going to try Ayan's mod and cross my fingers.