Hi! Better to write here if other people are interested maybe...
In Chisinau there is a youth hostel. I didn't go there so I do not know how it is. Even if there is not so much to see in Chisinau, or in Bucarest (this is my point of view) it can be nice to stay 2 days there.
In Moldova it s quite easy to travel by bus. Moldova is a really nice tiny country, with a beautiful countryside, full of sunflower fields in July... About the places to visit, I sugest to have a look in the lonely planet. About Roumania, I do not know so much about it because I did not stay so long. I would say that a really nice part is in the North, in Suceava, at the border with Moldova and Ukraine. I heard that other nice cities are Cluj and Brasov.
About Transnistria, I would say that it's better to avoid it, I am not sure
but I think that it is possible to go from Chisinau.
Actually there is a train between Bucarest and Chisnau, I would say that it leaves around 7pm/8pm.
For the interail pass, it ok to travel with it in europe, so until roumania and bulgaria it is fine. But it does work in Moldova. There is also a pass with eurolines.
Let me know if you need further information