it seems there is quite a bit of info lacking on the Gen 4 and Gen 5 stuff, that most experienced tuners know already because they started in the Gen 3 stuff and learned it there.
(any of you OG's who read this, please feel free to correct any of my posts if you see something that is not correct)
I understand that it's confusing and frustrating to read through all the Gen 3 stuff knowing most of it won't work with your Gen 4 setup, but there's a lot of good basic info there that will help.
i've also found that it helps to pull your factory tune, and play with it, compare it with others of your same engine/ecu/induction combination, see where things are different (compare feature is useful here) see where they are the same.
I'm definitely still on the learning side, though i have the advantage of using a few different types of tuning software on many different engines(megasquirt, apexi powerfc, subaru OS [ecutune/romraider]; Rotary, boxer, v6, v8). some extensively, some only a few small changes. knowing the basic steps of what to tune in what order is most important, and yet one of the most debated subjects.
When tuning ANY engine, personally I like to:
Get a basemap.
Something that will let the engine run and idle to operating temp, it is usually pig rich, and the timing everywhere is retarded a lot. idle is often high, and untuned.
Tune the VE/fueling
use a wideband, and info from forums, and others who regularly tune the engine you're tuning. they'll know roughly what lambda the engine likes to run at, and likes to make power at. Make your own decision on where you want your fueling ratios to be and tune for that ratio. Get ALL the cells you can tuned to this lambda, not just WOT (too many tuners in my area only tune a WOT pull, maybe 4 dyno pulls and call it tuned).
Tune the Spark advance.
use your knock sensors, or det cans, and best case a Dyno. Tune the spark advance in conditions you'll most likely be driving in. 80+ days means you don't want your iat to be 45 while tuning. on a dyno you can tune spark advance for max torque, while paying attention to the knock feedback/cans. if you get knock, pull some timing. Once you think you're done with the timing in all the cells you can, smooth the curve (no spikes, holes) and then pull a degree or three out for safety's sake.
Tune the VE again.
yes, again, though this time around it'll be much closer to where you want it, and if you have your VE and Injector settings correct, it truthfully shouldnt' have changed any reasonable amount.
Tune the spark advance again.
yes, again. (like above, it shouldn't have to change much, if at all)
Smooth graphs
go over all the maps/graphs you have changed, and make sure there are no holes/spikes in them, a well setup engine doesn't change VE/spark from one cell to a neighboring cell drastically, then back on the third.
Tune the Idle
Adjust idle timing/fueling to get the car to run smoothly at idle, some ECU's have separate idle control (most factory ECU's do) and that needs to be adjusted separately from the regular VE/Spark tuning.
Tune the startup
adjust the ASE (afterstart enrichment), priming pulse, cranking pulse, and other start related items to get the engine to crank and catch quickly while at operating temperature. On a rotary, this is very difficult.
Tune the Warmup enrichment/cold start enrichment
this one often takes the most time, and is very season dependant. adjust fueling offsets and enrichments at the temperature you are and above, until you get a smooth start and run. then if you'll likely never see colder, extrapolate and guess where it should be when colder just in case. It's difficult to tune when you only have one chance per day to log and adjust (maybe 2 if you don't have anything else to do) and let me tell you, on a rotary, this is also a pain
Go over my work again.
now because these ECU's have the PE (performance enrichment) we have to tune twice. once for out of PE, and once for in PE. out of PE is specifically designed for good fuel economy while keeping the engine alive, so it can be much more aggressive with leaning out the fueling (usually set to stoich). IN PE is where you want the engine to run safely, it's where you're beating on the engine, lot's of load, lot's of heat; so tune for it.
you'll hear a lot about Open and Closed loop tuning. these are really just different methods of tuning. Open loop is generally quicker, and better for the vehicle if you know what you're doing or if you've changed a lot of things that affect how the engine runs. BUT it costs more (wideband) and takes more care not to melt/destroy your engine. Closed loop takes the factory tuning corrections, and uses them as your telltale for adjusting things. it works well for small changes in how the engine runs, and is cheaper because it doesn't "Require" a wideband; but it takes a long time and if the tune is way off to begin with you may be melting/destroying your engine for a while till you get the tuning/logging/tuning/logging done.
I find dyno tuning is a lot like Open and Closed Loop tuning. on a dyno it's much easier to open loop tune, because you have full control of what the engine is doing and you don't have to care about being safe on the road. and usually it's cost prohibitive to rent a dyno for three solid days while you try to Closed loop tune on a dyno.
Without a dyno Closed loop tuning is easiest because you don't have to worry too much about if you're melting things. if setup anywhere close to where it should be the ECU will try and correct for the tuning discrepancies, and you log these to know where to adjust what. and renting the road is quite cheap when compared with renting a dyno.
hopefully this brings together a few of the basics, and helps you understand a bit more.