You are developing for Android without knowing where to find the logcat output?
It's available in the DDMS perspective in Eclipse. You should really check out your tools...
Serialized objects are briefly described in the wiki link that i gave you. Another desription:
http://www.jpct.net/forum2/index.php/topic,1578.msg11888.html#msg11888 jPCT doesn't care about "scenes"...for the loader, your OBJ-file is just a bunch of objects, which is why the loader returns an array of Object3D. You can either (de)serialize single objects or arrays of objects.
You can convert obj to 3ds with any tool that can do that. DeepExploration for example. If you still have that, give it a try.
I'm not sure what you mean with "in reverse". The coordinate system between jPCT and your editor may differ. Usually, a obj.rotateX((float) (-.5 * Math.PI)); should rotate the scene correctly. As said above, there is no "scene loading"...it just loads the objects from the file. The camera will remain default, unless you are changing it (i.e. located at the origin looking down the positive z-axis).