I am here assuming that you have sufficient knowledge to safely carry out basic tests on mains voltage equipment, but if you have any doubts about you own knowledge and qualification, get the unit tested by an electrician or electronic technician.
Never have the unit plugged in while the case is open (unless you are already a qualified electrician).
If you can post a couple of clear close-up pictures, it may help us to confirm your circuit description.
A few questions to get a clearer picture:
How do you know the transformer itself is faulty ?
Have you checked that the diode and the switch and the ammeter, and the connections between them and the transformer, are OK ?
Have you checked the fuse, if the unit (or it's plug) has one ?
What is your mains supply voltage, and what is the input voltage marked on the unit ?
Check the transformer by unplugging the unit, and connect a multimeter set to ohms across the mains input:
what does it read when the unit is switched between 6V and 12V ? If there are two readings, one about twice the other, the primary winding is OK. (Assuming any input fuse is OK, and that your circuit analysis is correct.)
With the unit unplugged and opened up, what is the meter reading across the secondary winding ?
If the exact transformer type is difficult to find, you may consider replacing it with a standard dual output 6V and 12V transformer, and modifying the circuit as per the attached standard circuit for such units. For this circuit, the type of transformer may be described as "12V centre-tapped" or "6-0-6V" or "6+6V", and for a 3A, 12V output, its power rating must be (at least) 36VA.
(Go higher with the power rating if you want your battery charged faster, but obviously within its limits. Car battery chargers are commonly up to 15A.)
Diodes are very cheap, just make sure their current and voltage rating is equal to, or above, what you are using them for, so have at least 25V diodes (as the peak voltage of the transformer output is about 1.5 times its nominal value).
Oh, and by the way, check whether you can buy a new charger unit for less than the cost of a replacement transformer !