Does anyone have any pictures that showed what Jonathan looked like before he died? I can't find any pictures of him later that suggest or confirm if they were taken shortly before his death, so I really don't know how he looked then.

There are several pictures of a Jonathan shortly before he died. If you go to YouTube and search for a video called Jonathan Brandis Gone Away you will see a few of them.
The pictures were taken after the premier of The Year a That Trembled September 11th 2003. They show Jonathan with a couple fans. One of them is the artist who sang the song Gone Away in the video. There is one picture of Jonathan by himself. That is reported to be the last picture ever taken of Jonathan. I have it on good authority that those pictures are available for purchase online. Buy you have to hunt to find them. FYI have a box of tissues handy, you will need them. There also several other videos by the same person. They are some of the best I have ever seen