A PCIII for a 04 6R will definitely not go on a 2001 model. The plug and play adapters won't fit and the engines are uh, very much different. The 01 is carbureted while the 04 is fuel injected. The PCIII's for the ZX6R and ZX6RR of the same year model are different even. You have to get a PCIII for your particular bike sorry.
To program it is easy as pie. You just have to install the software on a PC or laptop (Laptop would be better) and hook the USB up to the PCIII. The cord is pretty short so getting your PC near the bike is the difficult part. I just rolled it into the house. Grab a map off the official website that matches the specs of your slip on and load it onto the PCIII. If you want a custom tune you have to go to a motorcycle centre with a dyno and accredited smart people there to do it for you. It will cost you a pretty penny however. The maps on the official site are fine for a slip on. If you go full system you pretty much have to get a custom map.
Differences you will see are better fuel economy, more responsive throttle and an evening out of the power band. No surges in power. The bike will probably sound a lot happier too. Be sure to play around with the maps and tweak your idle after loading one.