Shasta,
I'm not sure I get what you're saying. You say you're going with MarkT pipes, trombones, etc but then ask if you should go with the stockers or stacks? Are you second guessing your decision?
I can't answer if you should get rid of your stock pipes but I do know if you do, MarkT is the way to go.
A few years back, I went with the MarkT Mild2Wild system and LOVED the sound.
I ordered the Miter Cut(Slash Cut) and went with the Organ Pipe silencers. I could go from almost stock to very loud(and very cool).
Here are a couple pics of my 38inch pipes with silencers in.


Here is a video of me doing some starts and going through the gears giving you an idea of what the pipes sound like in full trombone configuration. I think the microphone was inside my jacket to "try" to cut down on wind noise.
https://www.youtube.com/watch?v=A1s493a6BP0