Not sure if this will help, but I was able to get my program to export an ASCII file with vertex and triangle information about multiple models in a level. The file can be imported into MED as one model, then exported to 3DS or whatever format you need. I'd be happy to put some of the relevant parts of the code up here if you think it would help.

I used the MED export to ASCII to look at what the file should look like. I'm guessing you could do the same with an .obj file. One important thing I learned, is that you have to view the file in a hex editor, not just notepad. It had a bunch of otherwise invisible characters that it required for MED to read it properly.