"Its the bottom pipe that I can get secured. No matter how much prying (even used a jack) I cannot get this bolt.."
Do you mean to say--can not get secured--?
If the actual pump bolts are in I'd say you probably don't have the pipe seated all the way. I'd take it back off and give the seal a little smear of grease--then with the seal on the pipe--not the other way around---wiggle the pipe back into the pump.
I use the exact same method as Eric "planetman" -- and he and another poster mention using the correct top seals---Are you aware that there are two different sets of seals available? The difference being in the height of the seals--the taller meant for motors with the thick headgasket. Taller seals in place with the thinner headgasket could be a reason for difficulty getting the pump in place.-- Dave