Might be jumping in a little late and repeating a few points but just going to consolidate everything here.
2 main things:
Chamber 2 Plug
Return Pump
I'm assuming you have the plug in since it comes with both the InTank Media Basket 1 or 2. It's crucial since the Chamber 1 basket restricts the lateral flow from Chamber 1 to 2 by blocking the vents and forcing the flow downward vertically, which is ideal. A stronger return pump is going to help push everything more efficiently - the stock return pump is barely sufficient - plus your sps is gonna need the increased flow in your tank. This also makes any minor flow restriction from your media irrelevant. I upgraded to a Sicce .5 (Syncra Silent), it's nearly double the gph of the stock pump and works like a charm. The Eheim 1000 fits as well but the Sicce runs cooler so it's the better choice.
Chamber 1 water level will always sit above Chamber 2 of course, and Chamber 3 should be a little below 2, around the middle or just below the nut that secures your return on the inside of the chamber. My Chamber 3 water level typically sits at about 1.5 to 2 inches below the rim of the Tank. I'm guessing yours will be closer to 2 to 2.5 since your overflow gate isn't restricted so your Chamber 1 water level is lower than mine. If you choose to upgrade your pump (please, lol), just level the water in your filter until you have just a short drop off from your overflow, you only need enough to break surface tension, everything else should fall into place then you can fine tune. Add an ATO if you don't like to manually top off but with the stock hood (I don't run the cover on my filter normally) the evaporation is so minimal I don't think I'm putting more than a 1/2 cup of RO in daily.
As was mentioned by a few others, your filtration is redundant and you might be overdoing it. The Chemi-Blue has such a high level of phosphate absorption that running Phosguard with it is probably a bit much, you don't want to lower it to a point you actually starve your corals or have a dino outbreak. The Chemi-Blue also has carbon so your Purigen is really just for ammonia removal now (if you've got an issue) OR if you just need a little more polishing to catch smaller organic waste...but you've got plenty of floss doing it mechanically so not really necessary in my opinion to be a 24/7 thing and worry about the integrity of their bags and having to refresh the stuff monthly in Chlorine. You don't need all that extra full-time chemical filtration when you can easily just add a liquid ammonia neutralizer and do a water change or throw in a piece of Poly-Filter for a a few days or a week until you correct the issue then remove it.
Water changes are your friend right now. Do at least one 2 gallon water change a week, maybe even a 1 gallon mid week and a 2 gal on the weekend until your nitrates are down. You shouldn't need to worry too much about dosing because the frequent/adequate water changes with high quality salt will give you trace elements. Maybe invest in a Calcium testing kit, sounds like you have the rest.
Sorry for the novel, It's 3am and I'm wide awake for some reason. Just remember it's a 13 gallon tank, nano's aren't stable, and Murphy's Law is strong in this hobby.
You mentioned you still have the stock hood, have you done anything with lighting?
