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The pixel aspect ratio defaults have changed from CS3. They were close, now they're perfect.
On the resolution question, you'r misinterpreting the meaning of PPI. The only time that a PPI tag means anything at all is when an image is either placed in a publishing application (In Design, MSWord) and the only thing that the PPI tag controls is the size of the printed image. AE does not embed PPI info in images or image sequences. Changing the PPI from 72 to 9999 without resampling the image in Photoshop will not change anything but the printed size. Also, PPI doesn't understand pixel aspect ratios so when you take your DV or NTSC or PAL, or HDV pixel aspect ratio image into an app for printing, the image will be distorted.
The solution to the PAR and PPI problem if you need still images from AE is to always work in square pixels. Bring your non square footage into a square pixel equivalent sized comp and AE will make the proper adjustments. Square pixel equivalents for all non square formats are in the Composition Settings presets.
I'm not sure what's going on with your render. A bunch more info about the project is required. It's entirely possible that the settings on the CS3 version of your plug-in will need to be changed to make them work with the newer versions of the plug-in and newer version of AE. As for undo not working, it could be the same issue. A screen shot or more of a description of your project including render settings would help.
I understand what you're saying about the PPI. I didn't stop to think about that, the difference I saw in the res threw me off when I first saw it. The one important thing I forgot to mention is that there's now a slight shift, horzontally, from the center to the left and right sides in the imagery. That also leads me to wonder if it's the pixel aspect ratio causing it(1.21 vs. 1.2), between the 2 different version renders. This is causing me the most heartache because I'm needing to go in and change footage and make updates, but now I can't just render the changed portions because there'll be a jump in the imagery due to this. It's not the end of the world, as I can re-render the entire project (a little time consuming, but fine). Just hoping there was some quicker fix to what's happening as I'm thinking it'll be the case with all my other older projects. Plus, it would be nice to have a full understanding as to why there's the difference. Is it an Adobe CS upgrade that's the main culprit and that's just how it will be? I'm wondering if it's that and then the seperate plugin issue that may be the plug-in+AE upgrade difference.
I'll have to see if I can provide more info in a nice, clear manner along with some screen shots, as you suggest on Monday. For now, I need to call it a day!
This page and the resources that it points to explain the change in pixel aspect ratio (PAR) in CS4 applications and later: