I've found Chris' recipe to be pretty spot-on as to what I'm looking for in a a pastrami. I don't know if it was necessary to use a vac sealed bag to cure your flat but I can't really see how it could've hurt.
For dry cures, you're supposed to overhaul the bag once a day. That is: flip it around and end-to-end to redistribute the juices and solids that the curing process has released from the meat. Perhaps a vac-sealed bag wouldn't allow that redistribution?
I'm not sure how you went wrong, to be honest. Did you re-rub the flat after rinsing it? That is a very important step in getting a lot of flavor besides salt flavor into the final product.
You said the brisket flat had a lot of fat on, and that it didn't cure to red. These two factors are almost certainly related if you didn't trim the fat. Cure can't penetrate fat, or at least, not as efficiently as it penetrates lean meat.
One problem I've had with flats from costco is that they're mechanically separated from the point, I believe, and that several flats I've bought are actually a flat with a decent sized portion of point attached. You can "trim" the surface of the point but if you don't take it all the way off and trim that fat between the flat and the point there's no way the cure will penetrate the fat vein between them.
Give it another shot, following Chris' recipe to the letter, and see if it doesn't turn out better.