This is going to be a long read brother but my best advice for you. Depending on mileage and current condition of your car I would probably start by going over all the regular wear items suspension wise und upgrading those to suit your needs for daily/track use. After that I would go over the brakes. Those are going to help improve time/lap consistency, heat management for brakes, and driver confidence as you get familiar with the way your car handles on a track. Starting with bolt on power adders can often lead to brake fade and slower cornering speed. While extra horsepower sounds appealing, a stock car driven hard on a road course will quickly reveal that its factory stopping power and standard suspension are the weak links. Track driving puts immense thermal stress on a vehicle, and adding power before upgrading the chassis drastically accelerates component failure. Stock brake pads and fluid are designed for street use and will boil or glaze after a few hot laps. Upgrading to track oriented pads/fluid and upgrading brake lines will help keep braking power consistent. More power puts extra strain on factory axles, transmissions, and differentials. Upgrading the suspension helps transfer weight smoothly, reducing violent shock loads on your drivetrain. A car's track speed is ultimately limited by the size and quality of its tire contact patches, which suspension components are designed to optimize. Upgraded coilovers, stiffer sway bars, and adjustable camber plates keep the tires flat against the road/tarmac during hard cornering. Stiffer track suspension minimizes body roll, pitch, and dive. This stabilization keeps the car's weight distributed more evenly across all four tires. Replacing soft, rubber factory bushings with polyurethane or spherical bearings eliminates deflection, giving you immediate steering response. Tires and wheels also make a huge impact. Once all those things are addressed then I would do supporting mods like cooling mods. Upgraded radiator and adding an oil cooler. Then after those things are taken care you can get into the fun stuff and performance mods come into play. Depending on how much money you have to play with at this point would dictate the order in which I made those upgrades. Being budget conscious I’d start with exhaust and then intake. Adding a cat back first and then just collecting parts that will require a retune so I can do them at once and tune once vs adding a part here and there and tuning multiple times. If you made it this far I hope this advice can be of some help. Do some research of your own and you’ll find an approach that will suit your needs best!

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.

Could be flywheel. Is this a new noise since changing the trans? Could a bolt be loose and scraping somewhere? How's your input shaft look, any teeth missing? Also, may be silly, but the sound is definitely coming from the trans area?

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!

same stuff, unfortanately I'll have to settle with the jack the car comes with, I also carry a 3/8th drive and 1/2 drive electric impact and a set of sockets for both