28g JBJ issues

Ok, update time. The tank is now completely empty and dry, with the exception of the sump, which has maybe 1/4" of standing water in it, which is tap water from my cleanings. My wife and I were/am really bummed that we had to give up our 6 line and harlquin serpent star :(

My method after LR, LS, and livestock was removed was to let the tank run with tap water (about 26 gallons) and white vinegar (1.5 gallons). This ran for a week, and then equipment removed and cleaned with tap and elbow grease (all looks like new). The tank was emptied and filled with tap and emptied again several times to dilute the vinegar. Was nice to see the stubborn coraline just fall off of everything. The DT is immaculate now (thanks little fish for the vinegar suggestion).

I cannot seem to get all the water out of the sump, and there is also a little bit of gunk back there that I cannot get out becuase the area is hard to reach. I did baste and syphon out as much as I could though (a couple of times). It has a slight smell in the sump. I think the water will eventually evaporate since it has been so damn hot lately.

My next question for you guys relates to the sump. Since there is a little bit of gunk back there, maybe even some dead algae, will that cause problems when I start again? Maybe that will actually help kick start the new cycle? I can't seem to get the sump perfectly clean like the DT.
A shop vac will do wonders; just make sure there's no chemicals/crud on the sucking end and you're good to go.