I just did my water pump and broke off the one stud bolt i needed to put it all back together had to take the timing cover off which worked out good cause i found out i need to replace the timing chain and gears so it acutally might be a good idea to take it off just to see since you got it apart anyways better do it now than later and break off another bolt then 30 bucks and my truck runs great. also taking off the timing cover will let you get the bolt out unless it's broken off flush with the block which then i don't know how to help but someone will chime in that knows.

My two cents
Kyle