I had a similar situation putting my cap back on. It didn't line up perfectly with the old holes (to be expected), but managed to get a fit good enough all around to rivet/screw in place. My "stupid" moment was forgetting that the original tell tale sign that the floor/stringers were rotten was that the center of the the cap at the bow had sagged inward with no support underneath to the point that the center windshield wouldn't close.
It had been that way so long that the cap had taken a "set" in that position. I used a bottle jack up under the playpen to raise the center walkthrough/icechest area until the windshield would close & then attached aluminum angle brackets between the floor and bottom edge of the top cap in that area to hold things in place. That was a month ago & so far nothing's moved (the windshield gap is still the same) sitting in my garage.
If it's the walls of the hull that have drifted inward, you might try running some long screws from the outside, through the cap, into the hull wall to pull it out tight to the cap. Mine originally had alternating screws & rivets & that's what I went back with. The screws really helped pull the two pieces together in a few places before riveting.