@TWR, welcome here.
1) yes, airfilter off again, might still be clogged
2) yes, fuel might be contaminated with water,
remedy: syphoning out old stuff and refill, change fuelfilter too, when nearly empty put one liter of ethanol spirit in your tank (binds water) take it out then.
3) check up on
manualslib.com
Flood all motor and electronic/electric items on your scoot with WD 40, CARAMBA or similar.
Even switches and all plugs/connectors.
Sparkplug cap and ignition coil, check for sparking towards frame
Gear-oil has to be drained and refilled too, 'cause there is a high likelyhood of water via airfilter in it.
Feel free to ask further Qs, there's lots of people here who want to help.