These are some great tips.
I am extremely lazy when uploading. Since there are multiple sites on this server if I’m shelled in it’s to a separate user account, then su to root.
One thing to watch for if you do things the same way. you will need to chown the files back to the site owner and whatever group you use. If not, some things won’t work right. Plus, if you’re using quotas your numbers will be off if root owns any files in the site. You shouldn’t need to chmod them, as unzipping should retain the correct permissions on each file.
P.S. The first two things I install on any linux server I deploy are webmin, then MC (midnight commander). MC makes it MUCH easier to navigate and it has a great built in editor that color codes the text, has auto indent and a lot of other nifty features.
just my 0.02