After following the steps to upgrade (copying files over and running upgrade.php in the root) and going from 12 to 13,

I get this error "1045: Access denied for user 'seldondg'@'localhost' (using password: NO)"

I think didn't run upgrade.php and instead I ran the script directly in sql and that went in fine but when try to access my store it starts the new install procedure.

Any advice?

if it starts a new install procedure you must have the folder install on server remove that and it might work.

you might also need to edit your config file it also sounds like you have over written this and make sure your user n pass for database is correct.

I think you are right on.
I was so eager to install that I read
" a. Upload every file to the server replacing your existing ones excluding: "

as including instead of exluding. I had a backup made first so I'm just fixing it up now. What a dumb move.

LOL done it my self in the past just make backups before doing any upgrades and try keep a note of all the files you manaully edit so you can exclude them from futher upgrades etc.

That solved my problem. I still have my "no payment gateway" problem after using paypal express though.

have you setup your payment methods and made sure there active ? in admin then gateways.

I have it set in the gateways. What do you mean in the "admin"?
The payment goes through in paypal but when returning I get that gateway error.

I've got all of my payment issues worked out now.