I can't help you on the first matter, but as far as I remember I had no problems with unit transfers.
On the second matter, I agree with you in that PEST is just a tool, it can't build the model by itself.
As a tool, it is indeed helpful in highlighting the errors in the model: if it minimizes the RMS, and you're sure that it's the global minimum (not a local one), and you get unreasonable parameter values, than:
1. your head, flux or concentration measures are wrong
AND/OR
2. you're focusing only on some parameters, keeping fixed (i.e. considering well known) parameters that should be changed together with the first ones
AND/OR
3. your conceptual model is wrong, you're not simulating what really happens.
Unfortunately, PEST can't tell where's the problem, understanding the system's structure is all in our hands.
Good luck!
Giovanni Formentin