Yeah thats never any good , if theres not enough sticking out to get a hold of the timing cover will have to come off . Then you will have to work it out . There never easy .The bolt goes thru the pump & cover & screws into the block ...Lew
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
1991 F-150 ext cab 302 auto E40D 2wd. SOLD!!!!
1997 F-250 HD 7.3 PSD 4x4 auto. 6637 filter,rebuilt trans, Full 4" Diamond eye exhaust,Kitty ran away,Glowshift gauges.
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