I've finished fixing the rot problem. I used PT wood to rebuild under the walls and the door, so it shouldn't be an issue again, hopefully ever! I couldn't find a replacement aluminum threshold, so I built one out of oak and stained it to match the floor. I still have to install that, hopefullt tomorrow. I'm adding a 'skirt' to the bottom of the threshold to help keep the water from even touching
the aluminum siding. And I'll use lots of caulking in the right places this time. Whoever did it last didn't do very good job...but then that's par for the course I'm finding around here.
I installed the pine plank floor this week- it's stained and has 2 coats of varathane on it as well...will add 2 more I think. I used a preconditioner for the pine (Minwax), then (Behr)deck stain actually(chocolate), really easy to brush on, and none of that wiping off the excess mess! It worked great! Plus, it already has sealer in it...so I'm just adding satin varathane for extra protection.
Thank you fellas, for all your advice- I much appreciated it...even though it meant more work opening the floor...it was the right thing to do!