The Excel wheels that I have use brackets that have the same wheel fittings but not the same fitting bolt holes. Instead, the bracket has two fixing holes in the centre of the plates.
If the ones you have ordered are the same then you'll be drilling completely new holes nowhere near the existing ones.
Even if that's not the case then your thoughts on how to plug the 4 holes seem spot in to me. Lengths of quality birch dowel cut to be about an inch longer then the full depth of the block and transom would be my starting point.
I'd sand a very gentle taper to the end that is going in first and probably put it in from the side of the block so as to achieve the best possible finish on the inside where I'd see it the most.
I'd probably want a sufficient taper so that the dowel went at least half way through before snagging, then start tapping with a relatively light hammer via a wooden chock. My thought would be to tap the dowel through until it is 1mm shy of the transom face and then aim to cover that with some white sealant. On the exterior, the block, trim the dowel flush with a view to sanding the block and a quick lick of paint to seal and hide everything.
Even if your new brackets are the same as the old then this would still be the way that I'd plug the unwanted holes prior to drilling the new ones.
The density of the birch dowel will match the ply in the transom but it may be harder than the block, or the grain may be running a different way so I'd be extra vigilant when drilling the successive pilot holes as some of the early ones may be inclined to walk if they overlap the two woods.
The arms on my Excel wheels are possibly shorter than your current set up which meant I had to mount them quite a bit lower than where your block is. If you find yours are the same then obviously the existing block is redundant and it becomes more of a case of gently chiselling off the old blocks and bonding on longer ones to both take the new bracket and hide the old holes which I'd still plug as above.