At first glance, it looks like those "dents" are for box wrench fitment...but you say they're not on all the pipes. You could heat the dents and pry them out with a pry bar & short spacer.
My primary concern would be the bracket protrusion through the top of the ports because that's where most of the exhaust flow is. I'd grind those almost flush with the port roof.
May God's grace bless you in the Lord Jesus Christ.
'92 Ford Mustang GT: 385" SBF, Dart SHP 8.2 block, TFS TW 11R 205 heads, 11.8:1 comp, TFS R-Series intake, Dominator MPFI & DIS, 36-1 crank trigger/1x cam sync, 160A 3G alternator, Optima Red battery, A/C, 100HP progressive dry direct-port NOS, Spal dual 12" fans/3-core Frostbite aluminum radiator, Pypes dual 2.5" exhaust/off-road X-pipe/shorty headers, S&W subframe connectors, LenTech Strip Terminator wide-ratio AOD/2800 RPM converter, M4602G aluminum driveshaft, FRPP 3.31 gears, Cobra Trac-Lok differential, Moser 31 spline axles, '04 Cobra 4-disc brakes, '93 Cobra booster & M/C, 5-lug Bullitt wheels & 245/45R17 tires.