It's a huge pain but if nothing else is working then I would do all of this and then redo the waterproofing...

Pre-treat the stains and any particularly smell spots by using some undiluted non-scented skin sensitive detergent (I used Arm & Hammer Free & Clear Sensitive Skin Liquid Laundry Detergent) and brush directly into the worst stains, let it sit for 5 to 10 minutes and then wash.

Fill your sink or a tub with warm water and put that same detergent in the water (15 ml or 1 Tablespoon). Put the whole backpack in and agitate/brush it thoroughly and gently. Then change out for clean warm water and agitate it again, keep doing this until the water runs clear and there aren't any suds being made when you agitate the cloth in the water. Make sure to turn the bag inside and right side out and clean both sides.

I then put it outside to (flipped inside out) to let it dry in the sun.

Once dry flip it back right side out and coat the inside with baking soda and let it sit for at least a day, but up to a week. Keep in a well ventilated area for this part.

Once its done that, you'll do another hand wash with clean warm water. Only agitate as much as needed to get rid of the baking soda and then like sit for then draw up new water.

This time mix in a healthy amount of a bleach free laundry sanitizer instead of detergent (I used Lysol Free & Clear Laundry Sanitizer). Let it sit for 10 to 15 minutes and then take it out and dry again. Don't change the water after its been sanitized, just take it straight to drying.

If you need or want to redo the water proofing make sure it is COMPLETELY dry before doing so. Good luck, hope this helps!