I am in a similar situation as you and have already done some research on an m54 engine build out. I will answer what my research has shown me.
I agree with Toby; if you are building an m54, make sure it is the 3.0L version. aka the M54B30 engine. That engine already has forged rods and crank. How much power do you plan on running?
Here is what I have found so far:
Forged Pistons:
Mahle, CP, JE...... CP and JE can come in different sizes, so it all depends on how much machining you will do to the block. Mahle comes in one size. slight boring required. Stock bore is 84mm. Stock piston CR is 10.2:1 ..... You can also choose different CR's with the CP and JE pistons. or change CR with various cometic headgasket thicknesses.
Turbo Kit:
A lot of people run the CX Racing kit. its about $2200. I would suggest replacing some of the more important components with "brand name" ones. such as Wastegate, BOV, oil lines, and possibly the turbo. I do not have experience with cx racing turbos. Hell, they might be good. idk. All depends on your budget.
Tune:
Rk tunes - based in NY - ecu must be ms43
Kassel Performance - Based in PA - ms43 or ms45. I have talked to a couple of local guys that have had their ms45 ecu tuned by them. I have yet to call and discuss. Luckily for me I am only 40min from their shop.
If you are turboing you should really consider headstuds.
Headstuds:
Stock headBOLTS handle around 350hp
10mm studs handle up to 600hp
11mm studs handle over 600hp.
Cannot go to 12mm.
10mm kits:
Raceware -$350
ARP 202-5801 - $170 (this kit is not an official m54 kit, however I have read on the forums the studs are very similar in spec to the raceware and have reported success. I will be running arp when I build my spare engine.)
Another consideration when doing studs or bolts for that matter is to timesert the engine block. Because it is aluminum, it is a weaker material than the steel studs and the threads have a chance of pulling out under high boost applications.
Connecting Rods:
I know you didn't ask about this but I'll put the info here anyways.
The stock rods are forged. Hard to find info on power handling capabilities but I wrote down that they are good in the 400-500 ball park range. For my build (400 hp end goal @ the crank) that is cutting it too close without well documented research.
For peace of mind I am going with K1 or Eagle con rods. They can handle up to 1500hp. The con rod and con bolt kit (comes with arp bolts).Will run you less than 600. For me, that is insurance I am willing to pay.
Cams:
Schrick Cams - $1400
My personal opinion: Don't spend the money on cams if you are going forced induction. If you want more power, bump up the boooost
Injectors:
Rk tunes will provide you with injectors in their "tune kit". Check what size they are running.
That is all the info I have gathered. I hope this helps as a starting point. I would love to hear some input on compression ratio as I am still trying to figure out what would be a suitable number to run.
ps. reinforce your rear subframe before putting more power in this car.
Very important!!!