Is there a reason you can't use the rgl package instead (I'm not really familiar with rpanel, but I'm pretty sure that misc3d was originally design to work in conjunction with rgl) and use rgl.postscript(...,fmt="pdf") to export directly to PDF? rgl.postscript also offers an SVG option. The results are admittedly a little wonky sometimes (the underlying package it uses isn't completely reliable), but it's definitely the past of least resistance.
Also, I haven't tried it out myself, but I think the following article gives some information about embedding rgl images in their full, rotatable glory into PDFs: Levine, Richard A., Luke Tierney, Hadley Wickham, Eric Sampson, Dianne Cook, and David A. van Dyk. 2010. “Editorial: Publishing Animations, 3D Visualizations, and Movies in JCGS.” Journal of Computational and Graphical Statistics 19 (1) (January): 1–2. doi:10.1198/jcgs.2010.191ed. http://amstat.tandfonline.com/doi/abs/10.1198/jcgs.2010.191ed.