Hooooly crap... Sorry yea. real bad. You need to get another set of guide plates. If you cant find a good set that works properly then youll need a set of adjustable guide plates from ISKY. They only make a chevy set

. So youll need to slot them deeper for the fords.(dremel with a carbide bit) Then after you get them alinged then they need to be welded to hold the alingment. Tig weld if possible to avoid any splatter on your heads etc (ask me how i know...

)
Or you could just split your exsiting plates and weld those up. Harder to do as youd have to add a strip of steel to cover the gap.
Sigh sorry to be the bearer of bad news. I had to go through that also... What a pain.. But in the end i got it right and was much happier...
Good luck!