They are not too small to fertilize. Just be aware that every fertilizer company recommends a dosage rate way to high for young plants. They do it to sell more.. and trust me i work for one of the largest soil and fertilizer companies in the u.s. I would recommend feeding with half the recommend rate at first and slowly building up to full dosage..
I would guess your problem is simple. do a light flush and let them dry out. then feed em real light and slowly build up.. the fungus gnat issue isn't really an issue they are a pest but not a huge issue.. don't stress your plants trying to get rid of them. do it slowly they will go away. and on your next run just use preventive measures… I would recommend gnatrol. your all good though man dont trip.. it will all work it self out...