DG...Your certainly thinking.

If your 6L made more boost (at least 22/25psi) & just normal t. lag before CAC tube replaced & now only 20 psi, appears something wrong with how boot installed or ? Reflashing sounds wierd cause dont know about mpg, but your power loss was before, not after repair. Better luck on next visit. hmmmm?
btw..being under full 3yr/36K mi. warr. is good. Keep taking back until its fixed. Based on reports here (+mine) can take numerous trips to dealer.