Deck Drain Frustrations!

[TunaMeltdown]

Well After reading alot of archived material here going as far back as the sites begining I thought I knew all I needed to know about replacing the rear deck drains and the forward fish box thruhull in my 23' inboard. I was wrong. I ordered 170 dollars worth of moeller drain tubes, flanging tool, groco thru hull, and plenty of 5200 and started the demo process. Everything came out pretty well but thats about as far as I got. I bought 1" drain tubes because that is the original size that the boat came with (I think?) and someone in the boats 34 years of age hogged the holes to 1.25" . So my 1" drains will not work. Ok no problem I continue to the fish box drain, remove the plastic thru hull, dry fit the new brass groco, cut it to length and slather it in 5200 and put it in place. I tightened it from inside and jumped out to see how it looked on the outside and it was not seeted flush against the hull. Now I'm started to get really mad. The drain is located close to one of the chines and the mushroom on the thru hull is just to big. It seems to fit fine when you hold it in place but as you tighten the nut it will not seat properly? I'm kind of at my whits end here. I thought these would be simple replace ments and it seems I may have bit off more than I can chew. Any recommendations?
Thanks,
Dan Stewart.