@Philreedshikes thanks for the info. Good to know for future re-waterproofings.

@REI-JohnJ Sounds good, I am just following the directions outlined in the "Expert Advise" post: How to Waterproof a Tent. Anyways, here is the update:

First let me back up, I didn't post a "before" photo last time so here are some photos from before I resealed the seams:

Rainfly window seam (before)Rainfly window seam (before)Rainfly seam (before)Rainfly seam (before)

Of course, not all of the seams were so bad. This area was still in great condition (but not for long):

As I mentioned, I washed the whole thing in vinegar water (mostly water). Here are a couple of photos of that:
Rainfly acid (vinegar) rinseRainfly acid (vinegar) rinseRainfly acid (vinegar) rinseRainfly acid (vinegar) rinse

The first photo above shows the mildew on the rain fly. This acid rinse was an attempt to stop any further mildew growth and remove the smell. As you can see in the second photo, it was also quite effective at remove all of the rainfly sealing. On top of that, it delaminated the little velcro pieces and the strings for holding the doors open as those are apparently only held on with the sealant (consider yourself warned). I plan to seal these back on, although I think I lost some of the velcro straps. I ended up with 5, can anyone confirm how many there are supposed to be?

Okay so since my last post
I finished the remaining seals on the rainfly, then I coated the inside of the rainfly with  Gear Aid Seam Grip Tent Fabric Sealant:


In the first photo, half of a section is coated, and in the second, the whole section has been coated. This was the most difficult task because the applicator sponge is so small. As you can see in the second photo, I used a sponge paint brush to help spread the coating. Still, it was a pain. I was worried that I wasn't getting enough on and probably applied too much of this stuff. I did one section at a time to help keep track of where I had covered already - it dries as you. I did this on top of an old tanker desk covered with a plastic sheet to protect the desk and the tent. The coated area will be sticky until it is completely dry, so try to keep it away from dirty surface.

Not pictured, I recoated the inside of my tent bag, pole bag, and stake bag as well.

Finally, tonight I set up my rainfly and footprint in a nearby park and sprayed with Scotchgard (not much to see here - after photo only):

The directions on the back of the can said to mist the material with water as you apply the Scotchgard, which is why there is a spray bottle in my photo. Water beads up pretty nicely on the outside of the rainfly now. I did the in the park to avoid overspray in my garage (sorry grass).

So I have the rainfly + footprint ready for a backpacking trip this weekend! My final remaining tasks are to reseal the seams inside the floor of the tent, and re-coat the inside of the floor with the same tent fabric sealant that I used on the inside of the rainfly.

Total cost so far: $63
Total time spent so far: About 8 hours? Not really sure - haven't been tracking this closely.

More info on time:
The seams took a while, I'd say about 2 to 3 hours (you may be able to work faster on this). Coating the inside of the rainfly fabric probably took 2-4 hours across two different nights (I did one side the first night, then let it dry and did the other side the next night). Finally the Scotchgard application was very fast (10 minutes or so) but I had to go to the park and set up the rainfly, spray the Scotchgard, let it dry, break it down, take it home. That process took about an hour. So this comes out to a maximum of 8 hours so far. I probably have a few hours left to do the tent floor (luckily it is smaller than the rain fly). I wouldn't get into this unless you like projects like these kinds of projects.

Maybe some day I'll edit this into one nice, chronological, more coherent post...