Good question, and solid job laying out your current setup that helps a lot.

On an M54, a straight pipe where the rear muffler was will almost always introduce drone, especially cruising in the 2–3k RPM range. Even with a resonator up front, that motor tends to get boomy once you remove the rear muffler entirely, particularly on a dual setup.

If your goal is minimal drone, the Borla (or any quality straight-through muffler) is the safer move. You’ll still get a deeper, more aggressive tone over stock, but it stays controlled on the highway and won’t wear you out on longer drives. The M54 sounds best when it’s smooth and refined, not raw and raspy.

I was choosing headers for christmas and decided upon some "ebay" headers for the price. Never again lol. They worked fine but the issue was the quality control was non-existant. We had to cut the flanges off the headers and add more exhaust piping since they were not a "true fit" like the description said. I learned from that to always buy from reputable sources. They work so far, but I plan to get some better ones. What I would never change would be the addition of the underglow. It bring alot of character to the car!

I've been thinking about this all day and I'm thinking given the smaller aftermarket for that motor I'd probably start at the universal firsts. More, cooler air in and opening up the exhaust. Looks like Steeda carries an in-house intake for it that they sell as a "power pack" with a tune and they also carry a Magnaflow cat-back exhaust. That's probably the direction I would go to start with. Sway bars, end links, and frame stiffening are also almost never a bad idea. If you want to get a little fancier with the exhaust and maybe have access to a welder, you could totally look at building a more custom cat-back with a Valvetronics universal muffler or something similar. That would give you a quiet option as well as a loud, wide-open exhaust option when you want it. I love the valved system I put on my Corolla. It's rowdy when I want it to be but quiet enough not to wake my kiddo up when I leave for work at 5:30am.

Just 2 cents from a Toyota guy.

Good luck and happy building!