Having my 2004 Z4 M54 3.0i totaled was the worst, I miss that engine --- but the 2006 Z4 N52 3.0si has been good to me. Here is what I have learned. Also, I'm in Texas, so the suppliers I will list for parts/tune are in USA.
Skip to the bottom for power upgrades. And yes, do the sound generator mod, I recommend removing the larger of the two foam inserts.
Bought the car with 39,000 miles in 2014, today it is just a hair over 76,000 miles. Some mechanic tips: First thing was wheel bearings and CDV delete. For wheel bearings, buying the actual BMW special bearing press tool is the best thing I ever did. Next was the ZHP weighted shift knob. Hawk ceramic brake pads for low dust, or any of their performance pads are even better, USR black slotted rotors - do it. Next, one of the two DISA valves failed and my Oil Separator Valve needed replaced. DO NOT use the aluminum DISA rebuild kit from i6automotive. I did it to both large and small units, including buying formic acid to properly re-seal the valve enclosures... they were an utter failure with the extra weight - even testing them using the BMW factory diagnostic software proved they were problematic, just buy new DISAs. For lifter tapping, use Liqui-Moly hydraulic lifter additive, I've tried everything else with only consistent results from their product. Also, I recommend using their Ceratec treatment, it really does protect the engine if something like a water pump failure or coolant leak happens, or like me, the oil drain plug comes off a mile from home and you don't realize until you pull into the garage and the last 3 liters of oil pool under your car.
Power Upgrades, all done in the last 6 months after 4 years of no mods:
aFe Power Magnum Pro5 "Cold" air intake kit - this made a glorious difference to sounds and improves throttle response. It has a heat shield but I wouldn't necessarily call it "cold" air --- afepower.com
Bavarian Autosports high performance ignition coils - These make quite a noticeable difference in spark, revs drop faster which is wonderful for manual gearboxes. Even if you use the OEM spark plugs or NGK laser iridium upgrade, or the next item on my list, it is a better experience and there is a new level of howl and growl. Don't waste your money on other costly coil "upgrades" such as the brand name Ignition Projects, they are not better than BavAuto --- https://www.bavauto.com/mini-ignition-coil-5005
BERU racing spark plugs Part#FGR-6DDU - I am just telling you, with the better coils, these are unbelievably better than Bosch or NGK plugs, perform perfectly in extreme conditions both cold, wet or very hot including extended track use, these are in Turner Motorsport GT3 and other race cars.
Turner Motorsport ECU Tune - This is the real key to success, a tune which has been tweaked over long periods of racing N52 3-stage intake engines. Turner has a very valuable history of experience with this naturally aspirated i6, and the ECU tune for around $600 USD is by far worth the money. It is NOT to be used with aftermarket long tube headers, is meant to be run with the factory pre-cats, and they will give you different tunes depending on intake and exhaust cat-back or resonator/muffler mods. --- https://www.turnermotorsport.com/BMW-E85/c-30-performance-flash-software-2005-models
The combination of intake and ignition upgrades and this fuel/air/timing/throttle/DISA re-map (keep in mind my exhaust is fully stock), makes near as much 300 crank horsepower, and brings a bigger smile to my face than when I first bought it. It really is a new animal, and after 25 minutes of full chat on-track racing, flames begin to shoot out the back. (they must have added fuel to the areas on the map where air flow is reduced for engine cooling, when the exhaust is very hot and the fuel ignites, this is a great effect)