After the flies are out can you just go and ride it without harming the engine or you need to do additional work?
Yes. i did that with my 08 but felt no change in performance. I rode flies out without remapping fueling for thousands of miles. I think it was a full season. At least a couple months. The 06-07 bike has different stock fueling than the 08-11. Your 06 probably will be running lean up to 6000 rpm especially with the racing exhaust. That would be a concern to me but I never heard of anyone damaging their 06-07 by running flies out on stock fueling. I remember 06-07 owners saying just having the flies out without changing mapping made a big improvement in performance.
Is remapping something that you do on your own or you need a shop to do it for you?
Is a power commander a plug and play unit or you have to program it on your own if you install it after the flies are out?
Remapping can be done a few different ways. PC5, custom tune, Autotune, flash, Woolich software or some/all of the above.
If you are planning to go the PC5 rout, you will need to get a Power Commander. Also, you will need a PC5 map file (PC3 maps will not work if you get a PC5) for a 2006-2007 ZX-14 with flies out and your exact brand and model of exhaust. If you cannot find your exact exhaust, any full system should be closer than using a map for stock exhaust or slipons with flies out. Make sure you trust whoever you get that map from.
The PC5 is not hard to install but the plugs to the throttle bodies subharness are very difficult to separate. Other than connecting the PC5 inline to these plugs, all you need to do is connect the PC5 ground terminal to the frame and it is operational. If you do not have a map file in the PC5, it will not change the stock fueling at all. The map file is just a digital file that can be emailed. There are not that many owners out there who have PC5 maps they can share with you because they are not using the PC5s so much anymore. 06-07 bikes are also becoming pretty rare so I think you would need to get a PC5 map from a reputable tuner like Brock.
If I were you, I would order the PC5 from a reputable tuner like Brock and ask for a 06-07 ZX-14/flies out/race filter/2bros full system map. He won't have the 2bros map but he will give you his closest Brocks full system map. He can install his map to your PC5 before shipping it to you if you want and also email you the map or send it on disk---or all of the above if you ask. I would suggest getting familiar with the PC5 software. You could ask Dynojet to help you install the map by phone and interactive computer session if you like. Dynojet has free maps but I would not recommend using a Dynojet map. I am sure they are safe but not the best performance probably. You could try a Dynojet map but make sure you save the Brock's map so you can reload it if you prefer it which you probably will.
If you are running the bike at high altitude that could be a problem because most maps are made at sea level. If you are much more than a couple thousand feet above sea level and especially if you are experiencing poor performance with stock mapping, you might need a tuning shop to make a custom map. If you would rather tune yourself, you can get AutoTune for your PC5. It is complicated and dangerous but I have a tutorial on here that tells how to do it. A good shop can get similar results on the dynometer without breaking speed laws. Perfecting a dyno tune with a real world road tune is best though.
A lot of people get flashes these days. That is where the fueling and other ECU parameters are changed directly to your ECU. No PC5 is required but people who do flashes often still recommend using a PC5. That way, you can easily make changes to the mapping that was flashed to your ECU if needed. A flash is permanent and the only way to change it without using an external tuning device like a Power Commander is to have the ECU flashed again. Flashing is probably going to be the easiest way for you to get good tuning for the simple reason that flashing is probably the most common way to tune these days. Everyone is going with a flash. Not a lot of owners even know how to tune by module anymore. That was something that was a lot more common 10 years ago. You can still tune an 08-11 ZX-14 just as good with Dynojet modules as you can with flashing but the modules will cost you about $1200 by the time you get everything and a flash you can get for $300. ...but if you want to change it, you need to pull the ECU out and send it in for a reflash (probably free if you send it to the shop who flashed it initially) or use dynojet modules.
If you really want to go all the way, you can buy Woolich software and Woolich Autotune and flash tune your own ECU. That's not any cheaper than going with Dynojet products though.
My opinion is that if you own a 06-11 ZX-14, Dynojet modules offer the most flexibility and reliability. You can do everything to the 06-11 with DJ modules and a SpeedoHealer that a flash can do except turn on the cooling fan quicker. Also, you can custom tune.
It really all depends on how much time you want to spend learning about thois stuff, doomking. If you want fast and easy, a flash is the way to go. Put a PC5 on there later if you need it. You can always buy a used 06-07 ECU and have that flashed if you want to return totally to stock someday.
'08 MIDNIGHT SAPPHIRE BLUE Now Deceased