When I changed my 3.8L WP last fall, I chose to cut the thread lead in, off (about 1/4 inch) on those long studs that had nuts on them, that remain in the engine block & it'll give more room to remove the pump, without having to jack the engine up. I used my Dremel with a Harbor Freight Diamond wheel, that cut through that hardened steel like a hot knife through butter.
You may find that the head of one bolt, on the right hand side at about the 3 oclock position, as you look at the pump, will need to be passed under the lines that run along the top of the frame rail. Just raise & hold the lnes up a little, with a wooden wedge, to obtain clearance for the bolt head, to get the bolt in, or out.
I had the top bolt jam up on remaoval & had to grind that puppy out with a diamond bit from Harbor Freight, that fit my Dremel. took about 4 hours to do it & not mess up the aluminum casting's threads. That puppy didn't turn loose until I got the last little bit ground out.
I center punched the bolt & drilled through it with a 1/8 dia diamond drill bit, but it didn't turn loose with the heat & vibration of grinding. So I had to go back in & use the diamond bit as a grinding burr, to slowly open the drill through hole, just untill I could see the imprent of the crown of the aluminum castings threads, but not get into, or damage them.
Then pick the bolts remaining threads out.
Man that was fun & that danged bolt also just laughed at all of my strongest words of persuasion, humilation it was!!!! lol
Ford uses hardened steel in those bolts, so it'll be slow going if you have to grind them out & the casting they're in is aluminum, so be careful.
That danged bolt just laughed at all the heat & thread penetrants I used, including Liquid Wrench, PB blaster, Napatha, Fuel Oil, Marvel Oil, WD-40, ect
The Dealer had replaced the water pump back in 97 & I believe the Ford Tech cross threaded that top bolt, as all of the others came right out, no problem. Thank goodness it was the top one, as thats the easiest to get too!!!!
Hope you don't have the removal problems I did, with your broken WP bolt.
Be sure to use some anti-sieze on the bolts that thread into a blind hole & rtv on the threads on any you remove that thread into the water jacket!!!!
I bought all new Ford nuts & bolts for the replacement.
Hope you don't have to replace the WP metal extention tube connection for the lower radiator hose, as it'll be about $120 from the Dealer!!!!
On top of the old old WP, be sure to remove & save the small dia black pipe hose fitting that the engine/heater bypass hose connects too, so it can be used on the new pump.
I opted for a new ASC Signature Series WP from Advance, it has a lifetime warranty, was well machined & fit just like the OEM
one, for WAY less.
I did opt for a Felpro WP gasket though, as I didn't like the way the one that came with the new WP fit at the impeller.
A whole bunch more 3.8L WP thoughts for consideration. Let us know how it goes.