Hey Brandon, Might i also recommend that you see if your fuel tank has a drain on it.. Its possible that with 2 weeks of rain that your fuel cap (or some other nefarious reason) has somehow allowed water through and has accumulated to an unsuitable level where your separator cant handle the amount its sucking from the tank.
There is always going to be a certain amount of condensation build up in your tank over a period of time, the emptier it is, the more water you'll generate. the muck is usually a build up of rust and dust and crud from various other reasons (ie, quality of fuel, dispensation methods, etc) Bring in the water separator. from there, the secondary filter stops all the fun stuff that can be catastrophic to your fuel system's longevity.
you say the filters were full of water and muck? was it in both or just the one? I would definitely recommend having a peek in your tank. changing the filters is a requirement, but if your tank is dirty, it'll only be a matter of time till it does it again, costing you more than just a set of filters...
Edit: The fuel starvation caused by blocked filters would almost certainly Cause the white smoke you're experiencing.
Let us know how you get on, and good luck!