As far as the secret achievements go, I know a few of them through actually unlocking them and checking the list to see if they were on the x360a list. Majority of them are story related and cannot be missed.
Here's what I've got thus far:
"Cheque Please! (10G) - Survive the hit". Story related.
"I'm Just Getting Started (25G) - Find and interrogate Swifty". Story related.
"Decisions, Decisions (5G) - Refuse to cooperate with Victor in the Interrogation". When you're being interrogated and told to choose which of your guys gets killed, don't do anything.
"Escape the Brotherhood (25G) - Survive the interrogation". Story related.
"Storm the Mansion (25G) - Take back your mansion." Story related.
"One Flew Over... (20G) - Return to reality...?". Story related.
"Sweet Revenge (25G) - Avenge your Aunt Sarah". Story related.
"Date Night (25G) - Protect Jenny". Story related.
"Allies in Strange Places (20G) - Escape the asylum with help from the inside". Story related.
"Back in the Saddle (20G) - Rescue Jackie from the Iron Maiden". Story related.