That is a fairly "high tech" bike so even relatively simple operations might be a challenge if you don't know your way round your bike. ???
IMHO, it IS relevant that your ran tank dry. I've done this many times and seen results inside in the Carb, fuel pump or injectors, petcock and various filters. Right before you run dry your sucking up A LOT of crap of all kinds!
At this point it may not be cleared up with chemical additives, which often can help if used early on. You could also have WATER at bottom on your tank, and now WATER is in: 1. Fuel pump filter 2. fuel lines 3. Injectors
Spark Plugs will be fine. Leave them alone.
If you can I would remove fuel tank or at least remove the Petcock. Flush it out old fuel and check for debris. If you have access to your in line fuel filters, well, check them, clean if possible or replace.
Your fuel pump also should have some sort of internal filter. Some are cleanable or replaceable, some not. You can remove your fuel pump from fuel tank (it's inside of tank) Sometimes just flushing it out will help. Of course tank must be drained of fuel to do this. USE CAUTION HANDLING FUEL!
Water is easiest to remedy. A quality fuel additive can help absorb water in fuel and make it burnable.
Water, like debris, will settle to BOTTOM of your fuel tank, so running it DRY is not ideal as once water is in your injectors or fuel pump.
If you can, pre filter your fuel at fill up. I use Women's nylon stocking bits. Works great. I also run TWO in line filters plus the petcock has a filter. So, in all ... 3 filters. By far most effective is pre filtering fuel when filling up, using Nylon stocking.
Without this, this is what was lingering at bottom of my tank after just 2000 miles using suspect fuel.
This is only part of what was lurking at bottom of my tank and gathered round my Petcock. Lucky for me this did not affect the bike's running. But I never ran it near dry and I have an old DR650 with a Carb. So easy. Unstoppable.
Above is one of my 3 inline filters ... this tiny one is the last before fuel goes into Carb. Dirty but it still worked, bike ran.
With fuel injection you may not be so lucky. Most problems happen with the Fuel pump, which can sometimes be destroyed by crap collected. And if debris gets into injectors, they may need replacing.
With luck simple flushing your fuel system best you can may do the trick.
But at some point, you should do everything mentioned above and clean it all up, replace filters and such.
Good luck!