I would say the carpet and padding is definitely a place where odors could linger so it would help to remove it. Headliner is another reservoir but it would be best to leave it alone unless it will also be replaced. It is a difficult piece to remove and if it is fabric as used in most sedans instead of vinyl based as used in some hardtops, if you tried removal the fabric would probably be so rotten the thing would self destruct and be unusable afterwards. Even with the vinyl material the bow pockets may be rotten and split open. In many cases those could be repaired though.
One option might be to visit a few car detailing supply sites such as this one
https://psdetailproducts.com and look into one of the deodorant products that claims to encapsulate the odor molecules. Canada probably has a few sites and the products may even be sold locally thru a detailer.
The fact that a detailer can process a car suffering from years of cigarette smoke or other assorted odors and deliver it smelling like a new car speaks volumes for some of the formulations.
Something fairly easy and worth doing if they are in typical shape is the rubber edges on the flaps that shut off the air in the large ducts. By now most of the rubber forming the seal has hardened or some possibly cracked off and may not be completely closing the duct when the flaps are in the off position. In summer it may not be too noticeable but if you drive when it gets colder you will feel the draft when you do not want it. The flaps are relatively easy to remove and repair. The metal plates are stapled together and will need to come apart to replace the rubber but pop rivets or small screws can replace the staples. Steele sells die cut rubber pieces but as long as you follow the edge shape so it forms to the sides of the duct they are not too hard to make yourself out of 1/16" or so sheet rubber.
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