Those little flying bugs are fungus gnats.
More a pain in the arse than anything.
Problem is the adults lays about 200 eggs a day, so you don't need to many of them to piss ya off.
The adults feed on dead leaf matter and the larvae feed on the fine roots.
Established plants don't seem to be affected by them too much but I think they could do damage to seedling.
The coco-coir makes an attractive nesting ground because it's always moist but weather you get them or not depends on many things.
The benefits of growing in coco far out weigh these negatives though.
A coco grow is a 'drain to waste' affair too, so it may not suit everyone.
Never to late to trim the shitty bottom growth out.
3 weeks in sounds fine