For your exhaust woes, Id suggest a Buddy Club Spec 2. Its the ideal for an EP3 owner, nice and quiet on tickover, fairly smooth and quiet on journeys, and loud as hell when the VTEC barks. This coupled with a decent 4-2-1 manifold will give you some much needed low-end torque, and with a Hondata ECU (S200 seems to be a great unit), youll see that torque curve all through the rev range. The other great thing about the S200 is that there are so many programmes it can run. I read recently about an Accord Type-R owner who used it as his daily driver for the family, so didnt want the exhaust etc. He simply had the ECU mapped, so that only when the throttle was pressed with some determination would the VTEC activate. On a normal journey, the revs would rise above the VTEC actuation point, but the power curve would remain linear, rather than the massive hike usually associated with VTEC engines.
As for your brakes, there are two options. One is braided lines/uprated pads/ crossed/drilled rotors, and possibly some weight saving if you can live with it. The other is more expensive, but as you suggested, a big brake kit. I know for mine a ''big brake 310mm kit'' is around the £550 mark, although includes hoses/pads/lines etc. The next step up from that are 8-pots, which will rob of you around a grand in GBP. I would expect the EP3 to command similar prices. Four pots would more than suffice on a car like yours, though.
The lightened flywheel, coupled with a twin-plate clutch would be a healthy addition. On a daily drive in all honesty, the only real time you notice the flywheel is that it revs slightly free-er. A definite recommendation in my book.
As for the diff, I dont think you really need a good-spec diff unless youre planning on some track work. In all honesty, the same applies to the brakes. If you plan on seeing the track this year then thats excellent, although I would reccommend the weight-saving route first. I wouldnt want you to spend huge sums of money to dress the car up as something its not, thats all.
Other suggestions:
-Cams. Depending how much you use the car determines what duration to go for. I wouldnt go too wild, as the car will be lumpy as hell from idle, and will make the daily drive a nightmare.
-Coilovers. K-Sport do a cracking kit, fully adjustable as you'd expect, and for only around the £500 mark. Youll struggle to find better value for money. After my SX is sorted, theyre next on the wish-list.
-ITBs. This is a little OTT for road use, but I dont care what anyone says, the sound of a DOHC VTEC engine on ITBs is just as good as sex. Its also the only way to determine seeing 13s in on an N/A set-up.
-Wheels: Go for 15s. Ive only seen this once on an actual race-prepared EP3, they were Rota GT3s in red/polished lip, and they were 7inches wide. Not only do they look awesome when coupled with coilovers, but remember you have the achilles heel of FWD, once you start launching it like a man, wider wheels will help to eliminate scrabbling and the dreaded torque steer. These do look great with arch extensions too, as obviously at that width theyre going to stick out.
As for your initial question, Im afraid there isnt really a way to increase performance and maintain economy. Obviously making things more efficient is great with the likes of air filters/exhausts etc. But obviously (in a basic sense) to cope with this, the engine will add more fuel, thats just the way it goes. Dont be scared though, its not until you start getting daft that fuel consumption will become ridiculous. Besides, its always an anecdote, I always have people laughing at me for my whopping 9-11mpg. Hopefully a re-map will sort me out though...
At top gear they said it had the worst fuel economy they ever had in a car on their track. in consumed 1 littre within a Km wich is.... horrible.
and the userfriendlyness, cause I am not the only one who uses the car (although 95% of the time I am) and it has to have the lowest ricer level 
