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1000ms should be fine.
Your best debug tool here is probably a logic analyser to see the messaging going on over the serial lines, and the most pertinent UART Arduino code I've seen so far would be this blog post.
There is also this blog post for a different module, but it's not necessary to loop the config multiple times, you just need to confirm each message was sent properly (event message back) with the correct flow control (don't send while RTS is high).
If you use the reset pin to reset the chip, you should see the startup message come from the AP2 after it resets.
After all that it doesn't work, it's a possibility the AP2 might have been damaged from it's encounter with 5V directly...