I've decided to live with the Magnaflows for the time being. This is for a few reasons...
A. The engine tuning I had done mostly eliminated the exhaust popping and gurgling on decel. That helped the sound issue a bunch. So the sound is growing on me, or more accurately, is annoying me less. My friends tell me they like the sound from the outside. But it is still pretty obnoxious at high throttle.
B. I have more important issues at hand, #1 is getting the trans to work properly. Thought it was simply a programming issue, but now thinking it may be mechanical. Really need to get that sorted out first.
C. Still undecided if I'm going to keep this truck or just sell it.

What is your transmission issue?

How much time you got? :headspin:
It is a 6L80 that is supposed to be brand new. By the looks of it, I think it is new.
The main issue is it gets "lost" at light throttle, usually after decel, like when slowing for a railroad track or approaching a red light. Then when you lightly accelerate, it goes to downshift, then mid-downshift decides it needs to go back to upshift and bangs into the gear it just downshifted from. Goes back & forth...up/ down/ up/ down....I call it "lost". This continues til you accelerate enough to "forcefully" make it downshift with more throttle.
Took it to a tuner who found some upshift & downshift points that were set at the same speed. SO it appeared when he adjusted those points it would be cured. But all that did was change the speeds that it happens from the 30-40 mph range to the 50-60 mph range.
My tuner questioned whether there is a mechanical issue with the trans. I took it to a reputable trans shop in my area (owned by a street rodder). He scanned it (found no codes), and we went for a ride. It did the lost thing once during the test ride, but after it got really warm (over 180) it stopped doing it & I couldn't induce the issue. He thinks it is fine mechanically and it is a programming issue.
After I dropped him back at the shop, it did it again on my way home.
So it does this every time I drive it, mostly during warmup, but not always so.

Another issue is it has a very tight convertor in it...I'm guessing 1500 stall speed or so. The engine idles at 870-880 and is tugging at the convertor. So it is constantly trying to move the truck at idle. It will drive the truck at 7-8 mph at idle. It takes high brake pedal effort to hold it at a stop light and makes it tricky to pull into my garage with Racedeck matting.
GMPP recommends a 3200-3400 rpm convertor for the LS-3/ 480 hp. for auto trans applications.
I have a 3000-3200 convertor on order that should help this issue.
Once the convertor is installed, I think my next approach is to find someone who can simply install a stock ZL-1 program into my trans. and see where that takes us.
Thanks for asking. Always looking for someone who can steer me in the right direction.

I like my Borla XSPro’s on my Chevelle. I’m thinking about going with some Tesla mufflers however to quiet it down some.

I looked at a set of Tesla Turbos, but their range is too short for long cruises, and there aren't many superchargers around here.:headspin:

Do you have a stand alone controller for the trans? What brand?

No, the 6L80's have an internal TCU. Part of the valve body I'm told. There is a 15-ish wire harness going from the trans to the GM ECU so the engine & trans can communicate. That's about all I know about it at the time being.

I have/had something similar in my combo, coyote with 4R70w and simple shift command ecu. Trans builder said it’s the ecu the ecu company said it’s the trans. The trans builder back probed the w/h going from ecu to the trans ( where the shift signal comes from ) and proved that it shifts (at the screwy times) due to the ecu telling it to do so. The question then became why is the ecu telling it to shift. Right now I am leaning towards too narrow of a canbus signal from my gas pedal making inputs to the ecu way to sensative