Use McNett (or Gear Aid--same stuff and same mfr) Tent Sure Tent Floor Sealant to coat all sew-throughs on your pack, both inside and out.
Works amazingly well, as long as you have NOT sprayed the pack with DWR, which inhibits the adhesion of the sealant.
Most pack fabric is coated on one side (usually the inside) to prevent moisture ingress, but the waterproof urethane coating is penetrated at any sew-through, and so allows water it ingress. All those sew-throughs add-up. The stuff above fixes that. Not saying it will solve all your water-ingress problems, but if your pack has a lot of PALS webbing on it, the sealant will stop water ingress at all the sew-throughs. Spray the pack with DWR AFTER applying the Sealant. The DWR will shed water like crazy when new, and helps keep down the added weight of water.
Adds almost zero weight, and aids somewhat in preventing thread-unraveling where it is applied.
Something not mentioned yet, but all packs, pouches, and so forth should have appropriately-sized and located drain grommets, to allow water to drain, instead of remaining in the pack. Surprising how many packs/pouches/pockets and such lack drain grommets.