Hilmar,
You are perfectly right in the saying of s##t happens, it takes a certain kind of person to admit their mistakes publicly, and you are such a one, we can all learn from other peoples mistakes.
To get back to your little problem.
Now I have had a look at the cylinder, it looks like there is not much 'meat' left to play about with on the cylinder walls, even a sleeve might not do it.
To me, because you have gone so far, I would just carry on as you would have done if it was correct, and make no allowance anywhere else for the cylinders being offset, except for the fittings that go into the cylinder, top caps and crosshead guides should be made to fit the cylinders as though they were in the right place, as long as the screw holes don't break out or interfere with any porting.
As long as the base is correct, it would just mean that the cylinders are offset.
Not having the plans available to look at, it just might mean all you have to do is modify the bottom of the crosshead support, to take into account the changed geometry of the con rod swing, either by shortening slightly or putting a deeper countersink into the end, or a combination of both, to allow the con rod to swing without touching anywhere. Look at your crosshead guide drawing, and see if there is enough meat on the end to remove say 3/32" off the end and if you could get a slightly larger countersink in there. It might not run as perfectly as it should, because of the offset putting the geometry between the crank and the crosshead out slightly. But if you do try it, and it works OK, you will save yourself a load of cash, and you will end up with a unique engine with offset cylinders, a good selling point.
On the other hand, it just might mean I am talking thru my a##e, and there are too many items involved to go down that route. Without seeing the plans, and using basic knowledge of steam engines, this is the conclusion I came to.
I know it is of no consolation to you, but you can now see why I always mark things out, even though not needed, and make a machining schedule. Just a quick check before you put cutter to metal will tell you if major mistakes are going to happen.
I am not saying do it as I say, just consider it, it might mean a way around your problem, the choice in this case is totally yours.
John