Dave,
Depends what you mean by chip . The standard ECU is not programmable. Power Engineering do a replacement EPROM that allows remapping, but they are the only ones who remap the standard ECU. Other options are a replacement ECU (Motec, GEMS, Link) - only really recommended for engines with lots of modifications or competition cars. A piggy back ECU is another option, such as the Apexi stuff and HKS FCON. An external boost controller is needed (Blitz, HKS, Apexi) to control boost. Ralliart also do an uprated ECU (Sports ECU). Which is the best? Depends on what you intend doing. Everyone has a different opinion.
The conrod bolts are an alleged weak point in the engine when running boost pressure over 1.3 bar. This again has mixed opinion, bet I would say better to be safe than sorry. It is relatively low cost to do. The standard air filter is not that bad at all, but the exhaust is awful. An aftermarket exhaust will give you 30bhp on average. An induction kit will give you a little bit more. Recommend changing downpipe and de-cat too if you want lots of power. Be careful though - this freeing up of induction and exhaust will result in higher boost, and possibly fuel cuts - suggest you go with an ECU mod at the same time (PE/Ralliart Sports/Apexi)
Also alot of this depends on how you feel about warranties too!
The Stage 1 is not good value IMHO