I think I've done what you have. I had my stock muffler replaced with a custom welded Flowmaster Outlaw and that's it. I did not remove any of the resonators.
Other than a slight airy sound from the resonator at idle at the back of the truck, I don't hear any other sound. Is that the sound you are talking about? But I haven't noticed an engine tick you mentioned earlier.
I don't recommend removing the resonators, they do a good job in preventing drone inside the cab. If you want, you can get your muffler shop to simply weld the weep holes or you can just use JB weld, since you can dig it out later if you like, which is what a few members here have done. My shop actually mentioned they could fill that weep hole and move it further behind to make it hard to hear while still being functional.
Honestly, I don't notice the air coming from the weep holes anymore, just the awesome sound my Outlaw! I also don't hear any of it inside the cab, only when standing behind the truck.