You are correct. They now need not only the most recent tm 30 but also the completed set of rental contract, landlord's ID and landlord's house book or land ownership certificate ( Cha-nod.) This is new. Sometime last month, they needed just a tm.30 because in order to get a tm 30 you must have submitted those papers already. So basically you prepare the identical set twice now, one for tm 30 the other for yearly renewal. Noted that with or without agents assistance, the landlord paper set is always required.
The officers usually charge the agent 1000-1500 B for the late 90 day check in, no reciept. So it's normal for them to add an extra 1000 for themselves. Their service is that you don't have to go to immigration and your passport won't be stamped as having failed the 90 day report
When you transfer the stamps onto your new passport, the officer would handwrite down your previous passport number on your passport page. That would be a reference.
No Thai agents can assist you with US visas. The most they could do is application preparation or appointment time slots. US consular is notorious for granting/ refusing visas. Their piece of mind is every Thai applicants will certainly not return home if granted a US visa so your wife has to prove otherwise.
Technically your visa has ended on the day your money dropped below the requirements. At CW office, agents can sort this out provided that you add it back up to the 800K before you go to immigration.
The prices are used to be around
*****
extra to the officers, plus the usual 1900 fee, and the agent himself for the service is around 3000-4000.