Noworries and roll tide, welcome to the forum, good choice - with what you can learn here, pool ownership will be easier and your water will be better (the only downside is that your spouce will want to take an expensive vacation with all the money you save )
Noworries, you started out fine only adding 5/6 of what you thought was the recommended salt (aparently your pool is less than 24,000 - try using 5' as the av depth). The 2600 you first saw was the factory preset - every unit shows 2600 when you first turn it on - even if there is no salt in the pool. Where you lost your POP (pool owner patience) was when you added the other 100 lbs before verifying that the 1600 readout was accurate. With salt at 3900, the unit may decide that it doesn't want to make you chlorine (High salt light on steady means it won't generate, if the light is flashing the unit will still make chlorine but it'd prefer less). You can add more water to the pool to dilute it some (if the light is just flashing), though it seems to me that a partial drain and refill (using the 'plastic sheet method' discussed here will reduce the amt of water you need to drain).
I'm done scolding and will now (hopefully) enlighten you as to how to play with the generator. The number you see when you first open the controler is the average salinity over the last 100 minute cycle that the unit has run. If you get a 'screwy' number on the display pannel press the 'diagnostics' button next to the display 5 times
(what the presses represent, by # of press:
#1- Water temp
#2- voltage to cell
#3- Amps to cell
#4- % output -ie what the knob is set to
#5- Instant salinity (the ppm of salt in the water passing through the cell RIGHT NOW) for some reason it has a "-" in front of it))
(If the unit is not generating #2 - 5 will show as '0', when this happens turn the knob to 100 and wait a minute)
The 'instant salinity' is useful because it shows what's going on right now. Salt water is heavier than fresh water so if you've just gotten an inch of rain and only the skimmer is on, the salinity will show as low because you're pulling fresh water off the top of the pool. Always let the water circulate,constantly - drawing off the main drain, if applicable, for 24 hrs after adding salt before
making any more salt adjustments. Try to record the increase per bag when adding new salt the first few times, it'll give you a very good idea of your gallonage and what X lbs of salt adds to your pool.
I hope I've covered your ? but if you need more help, or just want to bounce an idea off of me, I'll be here -Waste

ps - did you add cya, if not get 5 lbs into a sock or a ladies 'knee high' (if you use the kneehigh it will probably take 2 to hold 5 lbs) and drop it in the skimmer (tie off the top so the cya doesn't escape).