In your reply, you gave some other key points. For one, you mentioned the house was unoccupied for some time. I would take that to mean that it was closed up for that period. Any house, closed and unoccupied for that period, will smell musty. I know my parents have a cabin in the mountains that is usually closed up for the winter, and when we would first use it in the spring, it would have a musty odor for a day or so. Sounds like you have an extreme case, probably more because it was closed up so long, than from the wet crawlspace. Do you plan to live there all the time, or is it a vacation home?
Try airing out the house as soon as the weather is nice. You need to dry out the house inside and out, so first chance open it all up and try to let it stay that way for several daytimes. Getting air movement will really help out. The mustiness is probably impregnated into your carpets, woodwork, and etc., so try shampooing the carpets, and cleaning all surfaces. While airing the house, open all internal doors and cabinets.
Besides things I have suggested already, here are some other suggestions, in the order I would do them if it were my place:
1 Re-insulate the crawlspace. Since you are in a cold region, the floor insulation is a good idea. Youíll want to replace any that is damp or smells bad, which probably means everything. You can use the same batt-type insulation that you removed. Just cover it (on the lower edge of the floor joists) with rigid insulated sheathing, which is about Ĺ inch thick. Problem is, the sheathing comes in 4X8 foot sheets, just like plywood, so I donít know how you would get it under the house without cutting it into strips, which would sort of defeats the purpose. There are some brands that come in 2 foot wide panels, if that will work. Otherwise, stapling a 7 mil poly wrap would do fine, and cost less. Just attach it to the lower edge of the floor joists. This is more work than just laying the plastic wrap on the dirt floor, but it will allow the dirt to ventilate better, while still providing a barrier between it and the house. The work will be easier with a power stapler, pneumatic or otherwise. Overlap the seams and donít bother taping. Of course, make all your joist replacement first, and any other plumbing/electrical repairs requiring work under the house. I would suggest removing all the old insulation first, then letting the wood dry out for a month or so while you make the wood, etc. repairs. A fan/dehumidifier under the house may speed the drying. Not having the insulation for the summer, and even the fall, is not a big issue since many homes have no insulation there to begin with. I would also make a chart showing where your existing plumbing/electrical/etc. is, so that you donít have to tear out everything to do a repair.
2 Contact a professional cleaning company that specializes in houses that have had a fire in them. They have products that neutralize the fire/chemical odor left behind after the fire. They should have something for your problem as well.
3 Replace the carpets and padding throughout the house.
4 Install an external French-drain system. Itís a great deal of work, and I would consider it as the last resort.
As always, I would also ask locals for their opinion. A neighbor may have had a similar problem, and came up with a different, but equally good solution. Also, your township and building inspector will offer good advise for your area.
Good luck, let me know what you end up doing - TomR