Going to be replacing an old Toshiba system with a new IP Office in the next few weeks. The system will be fed via 2 dedicated T1 circuits (not PRI). Currently, each circuit hits a CSU before going into the Toshiba system. Is it wise to leave these CSU's in place or can I simply go from the smartjack straight to the IPO? I am thinking that the IPO has in internal CSU builtin to the daughter card. Thoughts?

You are correct.
I would go smart jack to surge protection (If coming in on copper) to IPO.

Same here

Beings I do not currently have any soft of surge protection for a T1 circuit handy, what product would you recommend? Or maybe it is better off to leave the external CSU as a "first line of defense"?