Changed Exhaust manifold, now muffler won't fit

The D17 manifolds are interchangeable at the block with the WD and WD45 manifolds. The WD's and early 17's had a muffler that fit into the manifold and were held by a set screw bolt. The later 17s starting with series 3 used a bigger muffler that fit over a pipe sleeve screwed into a tapped hole in the manifold and the muffler fit over the sleeve and was held on with a common muffler clamp. The later system is considered better so some places sell this later system for both WD's and 17's. This is probably what happened to you. If your old muffler fit into the manifold, but the new manifold has a larger muffler hole that is tapped, then you need to get the chunk of pipe that fits into it and a either a new D17 s eries 3 muffler or an adapter sleeve to reduce down to the old muffler. The larger muffler required the hole in the hood to be enlarged. If that has not already been done, You may not want to do that and prefer to go with the reducer instead.
It is also possible you had the later system and have now reverted back to the early style.
It is also possible your old manifold was the WD type but had been reworked into the later style by welding a sleeve into it or reworked into something non standard.