This is an improvement to fuel mixture only. These bikes come out of the factory set very lean to pass EPA standards. This can be done with no modification to air filters, air boxes, or exhaust. What is involved is replacing ONLY the fuel metering needles in the carbs with a tapered needle (the straight is stock), and removing the plug from the idle mixture screw and enriching the idle mixture. This combination (richer needles & richer idle) will result in better running and power production from idle through mid-throttle range on an otherwise unmodified bike, or one with a mildly freer flowing exhaust such as a slip-on system (slip-on replaces mufflers only and not headpipes).
It is broadly recommended that you stay away from Stage I (and honestly all other) jet kits from DynoJet or Cobra (mfg by DynoJet). Their needle material is too hard and will unduly wear the emulsion tubes in the carbs, ultimately causing them to need replacement. I would seek out needles from Mikuni (the carb mfgr) or FactoryPro.
This essentially involves the steps in Stage I plus the addition of freer flowing air filters and richer main jets. Depending on your exhaust setup and the peculiarities of your bike, you may also need to bump up the pilot jets by one size. By far the most common setup is to go with K&N SU5589 air filters, which are a drop-in replacement for the Suzi filters, and to up the main jets from the current 90/100 front/rear to 125/135 (122.5/132.5 - 127.5/137.5 is the common size range at stage II).
In my bike I have a stage II setup as follows - K&Ns as above, 125/135 front/rear main jets, Mikuni needles with the clips at position 3 front and rear, mixture screws at 2.5 turns out front/rear, 42.5/52.5 pilot jets (one size up from stock), and Cobra slashcut slipon exhaust. Runs phenominally, pulls hard throughout the throttle range, and still gets 50mpg on the back roads when I go easy on it.
This involves removing the airboxes and replacing with clamp-on filters (usually K&Ns), needles, mixture screws, MUCH larger main jets (usually 145/155 or above depending on exhaust), bigger pilot jets, etc. This is a serious upgrade and requires much tuning to get it right on a particular bike. It really is most advantageous when done with very free-flowing exhausts like full systems or drag type slip-ons.
I strongly recommend that if you're considering rejetting your Marauder, you see Spacer Jim's Jetting Information page and post your questions on the MIG Delphi Forum. There are a lot of folks over there who have successfully accomplished this upgrade. There's no black art here, and stage II is the best single performance improvement you can make on the Marauder. Spacer Jim on the Forum sells jet kits for Stage II on his site and, along withe the other members, can provide lots of good advice. Jim also sells a kit of top-quality stainless steel screws to replace the garbage screws that are stock in the carbs and will undoubtedly be destroyed when you take it apart.