Thanks all...I know it's cheating but I think I'm going to go with the glue option. I have a hot glue gun is that preferrable or is the Shoe Goo option better?
I use Shoe Goo quite often and have for years. I will vouch for it being very good stuff. In regard to patches, I use Shoe Goo to glue the velcro to the back of the patches I use on the Fatboy. Strong stuff, and good for that sort of thing.But, I would advise you to just stitch your patches on the Timbuk and go right through the liner. Just do a neat job and use good thread. You won't see water come through the stitches, at least I never did. My old Timbuk saw many years of heavy rain.. day after day.. on the bike and off, and I had pins and patches both that penetrated through the two layers. So did many of my messenger pals, and nobody complained of water coming through. If it worries you that much, after you stitch it on, I suppose you could seal over the patch stitching on the inside with duct tape or some kind of sealant. I like the wax idea too.I even had my old bag develop so much wear that the liner split in places, and I still never had wet cargo. I've seen bikers with the liner on all brands of well used bags fixed with duct tape, and they were working.. so it must have been fine or else they'd have had wet packages. If I could survive three winters and three springs on the bike 5 days a week with pin holes and stitching in mine, I suspect you'll be just fine.