I'll try to give an undetailed overview of v-tune.
You set a copy of your calibration to go closed-loop in as much of the fuel table as you're allowed to do so. You use a target value which is near the rich end of the available closed-loop range for the sake of the engine. The instructions are totally unambiguous regarding this, so you can just blindly follow them.
You effectively disable the PE override mode which adds fuel over time under high load to help cool the engine. It's a good thing in normal use but when activated will halt vtune data collection, making for wasted time, and you're not going to be running that way much if at all while v-tuning.
You load the calibration into the ECM, start a "v-tune data" logging session and go for a ride. While riding you avoid sudden throttle changes and try your best to "feel" your way through as much of the VE tables as possible. You'll definitely not get all areas but that's okay. Get as much as you can. When done, you use the v-tune software to generate a separate calibration using the data you acquired against the calibration in use to fetch it.
You then load that new calibration and gather more data.
A few iterations are generally sufficient when you start out close, as you will be doing. You may look at the first one and say "This is going to be a waste of time" if proposed changes are few and minor.
You then take the last-made calibration and restore the PE and fuelling values to original, save it, then load it. Done!
While v-tune data logging some folks like to also disable Acceleration Enrichment and (I think not so much) Deceleration Enleanment, both of which are brought into play with sudden/rapid changes in throttle. While these modes are active (they're phased out over time following the event), data being gathered is ignored. The notion is by disabling them you get more data. That is certainly true, however I'm of the opinion that some of the data (notably the initial part of it each time) now being retained isn't so good because if AE, say, were called for but not supplied, the engine will be acting slightly lean, with the opposite for DE. If you make decisive and relatively few throttle changes you can overwhelm those few (now-collected) funky data points with some extra good data. But if you're not particularly decisive about being not smooth it's possible to grab a bunch of funky data which will be dutifully used afterward since it wasn't thrown out.
I'd rather spend a couple extra minutes gathering data and know that it's all good, so I leave those modes enabled while v-tuning.
There are other factors to look at while finishing the whole process, namely blending of the resultant VE tables, but let's go over that when the time comes. You may not need to do it...
Polishing your calibration for your specific stuff will be rewarding. In your case you likely only need to correct for the fact that fuel injectors are similar to snowflakes: no two behave exactly alike in all aspects. The two you have are going to be some different from each other and neither will be/do exactly the same as either of the two in the bike Steve used to generate the calibration.