Was it rendering Targa files or a Targa sequence? It's always a good idea to render an image sequence out of your 3d software instead of a video file. That way, if something goes wrong in the render, you only have to render the frames that it hasn't completed. If you render right into a video file, you could have a render that goes on over an entire weekend and have nothing to show for it on Monday morning if it glitches on the final frame.
Also, I would recommend a PNG sequence over Targa - I don't know anybody who uses Targa anymore. When importing, choose any of your images (be they Targa, TIFF, JPG, or PNG) and tick the little box in the lower left of the import dialog to let AE know that it's an image sequence. Voila! You'll have what behaves like a video in AE. You may need to specify a particular frame rate in the Interpret Footage dialog to make it match up right.
Do you have masks on your 3d render or on the footage of your friend? IF it's on the footage, you should be able to replace the Targa still with your footage without any issues.
If you have masks on the windmill render, you should be able to copy and paste them onto the new footage (or just replace the old footage with new footage...)
When I looked up how to get my 3d stuff into After Effects, I found the compositor link process, the only problem was there was never a lot of info or help on how to do it, so I was forced to experiment and learn it on my own. Eventually I got it to work, obviously. I think 3ds Max automatically chooses a TGA file when you render the states, so since I had no idea what I was doing, I went along with it. Thanks for the info though, I will try it with PNG next time instead. Also, since I had I think 300 frames, it automatically rendered it as separate image files, but I didn't see any "sequence" option when I did it, so I guess maybe it does it on it's own? I did go to the render options today though and I did find a "sequence" option, it was blacked out however. If 3ds Max is rendering as separate image files anyway, do I still need to click a sequence option? I would of thought as long as they're multiple image files, a sequence is basically the same thing, no?
After I had 300 TGA image files, not knowing that I could import them straight into After Effects like you said, I went into Premier and was able to import those files to make it a video. I did have them set to 60 frames in 3ds Max, at least where I think is the correct spot to set them as such, pretty sure it was.... but when I previewed it in Premier it was 30 frames, which is not what I want. I ended up deleting all those TGA's out of frustration before I came here.
I think I've looked around in the Interpret Footage dialog before, but I'm not familiar with it, I guess I have to look into it some more.
Lastly, my masks in After Effects are on the Village_Output.tga, which is the file 3ds Max sends to After Effects (basically the render file). So I would have to go with this copy and paste option, which where I'm used to right clicking for copy/paste, I couldn't find out where to copy the masks so I made this post. So if you know how to copy/paste masks that would be helpful! Also, if I was to change the Village_Output.tga to a PNG to make it Village_Output.png, I think through the Autodesk Link it will still only display the final frame (most likely because of the fact I can't click that sequence option). So I'm assuming I would have to render the 300 frames as PNG images, then import them into Premier and make it a video, then send it to After Effects?
Thanks for the help you've given so far, hopefully I can get this to work in the end.