Having 'staged' both my Harleys (carbed and EFi), I would make the following points:
1. You will see an improvement in power output (mostly peak) after making a stage 1 upgrade.
2. The bike will run a little richer and cooler and better. Modern Harley's are setup to run lean (and very hot).
3. If you only change the silencers, then you won't need to change anything else on the bike.
4. If you swap out the whole exhaust, then you will need to do a proper stage 1 (air filter, fuelling and pipes). This is more expensive.
5. You can pick up parts used on ebay over time, this will save you money.
6. If you want to change all components, it won't matter too much what bits you choose, there are very rarely any major compatibility issues.
7. Air Filter - it's all about increasing the flow, the housing is just 'bling'. (I went for a hi-flow K&N that fit under my stock housing, relatively 'cheap').
8. Fuelling - XIED or a V&H fuel pak is simple, but crude. Personally, I would buy a something like a Power Commander as most dyno places can set them up for you without too much hassle.
9. Pipes - Personally I like 2:1 systems, but it's totally your call. V&H Short Shots are very common, I'd say too common, but it's a personal taste thing.
10. Budget - it can be anything from a few hundred to around £1500.
11. Stage 2 - just to confuse the issue, you will see the most benefit from fitting news cams to a stage 1 bike. The cost is not too much more (few hundred) and the increase in performance will be massive. You won't regret it.
Hope this helps.