With larger injectors and an AFC, you won't be over-pressurizing your fuel system, and it will considerably a bit better than an FMU setup. For the best results, you would need to tune it on a dyno. If you run 450cc injectors, you don't need check valves or a missing link becasue you trim the MAP signal with the AFC. You start off by setting your fuel trim to -40% across the board until you can get it tuned. This negative value fuel enrichment(in reality it would be fuel trim, since you're cutting the MAP signal), you're lowering the MAP sensor signal enough to allow you to boost without using any MAP limiting devices(voltage clamp, check valve, missing link). As long as you stay below 10-12lbs of boost, you won't throw a MAP code. This aaplies to 440-450cc injectors. If you go with smaller injectors, your fuel trim will be less, so it may not allow you to run the AFC "hack" in this fashion. The reason I keep mentioning DSM 450cc injectors is because they're relatively cheap, and easy to come by since DSM owners usually upgrde theyr injectors and have no use for they stocks. If you get RC injectors, even if you get the saturated ones, you'll still need to convert to OBD-I injector clips, and the RC ones are solder-in type. There are some new direct replacemtn injector adaptors that were just developed, and they simply plug into your stock injector clips and adapt them to OBD-I. A guy named Viren(b18bturbo) on Honda-Tech sells them for $10 a piece, I believe. If you get peak and hold injectors(like the DSMs), which are usually cheaper than saturated, then you'll need the resistor box. Hondata and EMS both basically have the same features, so which one is "better" would be up to you. Hondata is pretty well known to tuners, and it wouldn't be hard for you to find a good tuner. EMS is a newer system, and while there are good tuners out there, it can be difficult to even get your car started unless you can find a decent basemap. EMS replaces your OEM ECM completely and plugs directly into your harness. Both Hondata and EMS cost about the same if you figure EMS costs about $1200, and an S200 system with all the bells and whistles, along with an OBD-I ECM and adapter harness would also cost about that much. For simplicity, the EMS would probably be better, since you don't need to have an interface box like the Hondata units. EMS also comes with all the features like 3-step rev limiter, datalogging, full throttle shift, auto-tune, etc already included, whereas with Hondata they're offered as modular "upgrades" which is what drives up the initial cost of the S200 w/ boost system($495 for S200 w/boost and no extra features) to about the same amount as the EMS. You also don't need a ROM burner or emulator to make changes to the EMS, so there's another advantage. If you're willing to take the time to leanr how to use the EMS, it's a great system, but some people don't have the greatest of luck with it right off the bat, get discouraged, and switch to Hondata.

As for your pump being noisy, it has been my experience that inline pumps are usually pretty noisy. Mine was mounted on the firewall when I was running an FMU setup, and that thing would whine like nothing else. I got used to it, and I actually grew to like it, somewhat. Now, if your pump is making noises that it wasn't making before, then I would be concerned.