K&N makes a Filtercharger reusable air filter for the SHO at about $40. It fits, albeit snugly, into the stock filter box, and is claimed to flow much more air than a similarly sized paper air filter. (There are occasional flame wars on this topic in the various rec.autos newsgroups.) Periodic cleaning and oiling with K&N filter oil is required. Emissions legal.
Caution: Oil impregnated filters
Some users of the oil-impregnated filters, such as the K&N, have gotten a bit over-zealous when oiling the element and the excess oil coats the measurement resistor wires in the Mass Air Flow sensor. The oil acts as an insulator, causing the sensor to output a signal that indicates that there is less air entering the engine then is actually flowing through the sensor, resulting in a dangerously lean fuel/air mix. Since the Ford (Hitachi) MAF doesn't have a high temp wire-cleaning cycle, like the Bosch hot wire meters, the oil coating never gets burned off.
EEC-IV will complain only if the sensor output gets more than 20% away from where EEC thinks it should be. EEC uses the MAF and the crank sensor to calculate an engine load number, which ultimately results in a fuel injector pulse width. When running in closed-loop strategy, the mixture would be corrected using the exhaust gas sensors and no problems would result. If, during closed loop, EEC sees that it needs to enrich the fuel beyond normal limits for the RPM, MAF, and engine coolant temperature signals that it's seeing, it may set a code for MAF signal out-of-range or fuel enriched beyond normal limits. However, open-loop strategies, such as wide open throttle, don't use the HEGOs, so the mixture could run lean, because the MAF output signal is reading less air then is actually entering the engine. MAF reads air in mass-per-unit-time, so a low reading vs. RPM tells EEC that you're ingesting less dense air, and the fuel mixture is leaned accordingly. If the MAF/RPM load number and the barometric pressure (BAP) signal don't make sense to EEC, then a BAP out-of-range code might get set. At any rate, lean mixtures at WOT can lead to catalytic converter overheating and subsequent damage.
MAF Element Cleaning
The best way to clean the wires would be to remove the sensor module from the body and carefully spray the wires with a good solvent, such as carburetor cleaner.
K&N's instructions are pretty specific about not over-oiling the filter. The K&N is a great filter as long as its maintained properly. Clean and re-oil it about every 10K miles.
I've never seen any independent test data as to whether the K&N is better at trapping dirt than the Motorcraft paper filter. Since K&N has a product to sell, their results should be subject to some healthy skepticism. Additionally, the K&N is not really a performance mod: the difference between the paper filter and no filter is less than 4HP, which is in the noise on most chassis dynos. Also, the pressure drops vs. the K&N and stock paper filters for reasonable flows* are difficult to distinguish.
* - Reasonable being 400cfm, which the Yamamotor wants at 7500 RPM. One of K&N's ads shows a panel filter flowing 887cfm, which equates to 17,000 RPM on a 3.0L motor, or 6750 RPM on a 454 c.i.d. V8. Either example is a scattered engine.