Have you ever wondered why your tuner is specific on what injectors you have in your vehicle? Here's some simplistic reasons for you. When it comes to tuning, it's not just about HP gains, it's about drive-ability as well. Wide open pulls is not the hard part, it is the part throttle, starting, and everything but wide open throttle tuning that requires more attention and detail. For your tuner to get this part completed in an efficient way, they have specific injectors they use based off of experience.
What's the difference between brands? Well, quality is a big factor here, but injector data is one of the biggest factors as well. Quality and data will typically come hand- in hand. This data is information already from the injector company based on how they tested and flow their injectors. Flow rates and voltage settings is some information that the tuner needs for the tune to be more accurate for better drive-ability. You want to make sure each cylinder is getting equivalent fueling for it to perform properly. Having this data accessible at any point in time is also a big factor. Some companies make you email them for data, and they are not available 24/7, so it affects the timing of when the tune can be completed.
Size, is also a big factor when it comes to injector selection. Each tuner has their preference as to what injector duty cycle they want to be working with each individual build. This mean the percentage of available injector left to the atmosphere to change. If you are over working an injector, it is likely that it won't be able to perform at times, and can be catastrophic to your engine. Leaving some percentage open for the injector to work gives your fuel system some "cushion". Just because something "can" run, doesn't mean that each tuner will work that way. Also, when it comes to size, if you know you are planning on adding more power in the future, be prepared to purchase a larger injector at that time so you aren't having to purchase twice.
Parts you found off of eBay, or one your friend pulls out of his garage is probably something you want to stay away from. Companies that have great data, and use quality testing/flow tools is something you want to purchase, but consult with your tuner before you purchase ANY fueling components for your vehicle. If you are unaware of what injectors you have installed in your vehicle, that mean's your tuner probably doesn't know that information as well. Drive-ability issues, like stumbling, bad gas mileage, bad startups, and delayed fueling can be caused by bad injectors, or simply not tuned for the correct fueling, and injector data.