The way to help with (3) would be to make sure that the file you upload starts at exactly the same spot as the file TNG uploaded. Like, exactly. Last time, your two files didn't even start in the same place. You should be able to import what you upload into a new project right next to the old project and hear no flanging, no phasing, no delay, nothing. Theoretically you should be able to invert phase on one track and have it cancel out the other. ptf is a pro tools project format. It's old. It's what TNG uses. The rest of us moved on to .ptx like 4 years ago.
Dammit! I forgot the clap. Next time. I'll send the PTF tonight after some House of Cards. Way behind in that department and from what I've seen, it's a pretty stellar second season. Edit: will send tomorrow
So I use Audacity because it's free. What I do is export the audio of the previous file with mine. I then delete the track that isn't mine, and export my isolated track that way. How it doesn't line up then is besides me. Any suggestions?
Whelp, this is why I suggested TNG post every track he starts with an audible "Click" so that I can line it up. Because beyond that, Audacity is just barely better than nothing. Things substantially better than nothing, and also free?
Use both. Figure out which one works better for you. I'm gonna guess Reaper; it has a lot of proponents and Pro Tools Free is even more cut down than Pro Tools, which is virtually useless compared to Pro Tools HD. Which costs an eye-popping amount of money for someone used to "free." I have plugins that cost $900.