Last October, after being unable to prove my monthly pension payments were coming from abroad, I obtained a 1-year ME to visit my thai wife at Sawannakhet. My question is this:

Now that I've sorted out the proof of international transfers (thanks to Transferwise), can I now apply for a 1-year extension with proof of 2 monthly payments of over 40,000 baht into my bank account or will I need 12 payments?

You could apply for the extension now.

Just be sure you have proof the transfers came from abroad. 

Thanks Joe. I've got all the necessary proofs. I'll wait until the amnesty is over before applying.