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Without repairing the source of the water intrusion anything that you do is just going to be a temporary bandaid. If there is mold present on any of the wood members it can be sealed with Kilz Original. Ideally any moldy materials should be replaced, but if this is not possible then the next best option is to use a sealant. All of the affected building materials must be dried completely though. The use of a dehumidifier is a good start. If you have a moisture meter available it will be able to measure the moisture content in the wood and determine when it is effectively dried.

The flashing being completely rusted could be stabilized by nailing a new piece of flashing up against the existing. It will not be very effective in repelling water but will provide some stability to the rusted flashing. New insulation can be put in place as well.

I would recommend trying to locate the source of the water intrusion on the exterior. Whether it be a roof leak or cracks in the exterior wall. Cracks could be addressed with an exterior sealant or a roof repair may be necessary.

My concern is that just "fixing" what is there will result in doing the whole process again at a later time.