Paint the flooring with KILZ. it'll seal the floor and will help prevent any more allergens. You can get it at any big box home store.

If you have severe allergies carpet is the worst choice for flooring. Anything else - hardwood, laminate, vinyl - is better. Yes, you could have an invisible mold problem someplace causing your problems. I suspect that it was the pulling up the carpet and padding, though, putting all the previously trapped dust, polle, and mold spores into the air.

Thank you both. I think it was pulling up the old dirty carpet and padding. Wish I could have gone with laminate or vinyl but that wasn't possible. Again thanks for your input.

Can you try getting you air ducts cleaned?