That’s too bad. The System i runs Domino much better than any Windows box ever will, but I am sure you don’t need a lecture.
You will of course need to move the DATA folder off of your System i to you new Domino server. So create the Domino Server on the Windows box and then you can just copy and past if over from the IFS. I don’t know if any problems. I would however use this opportunity to clean up as much as you can and then make sure you are doing COMPACTS and FIXUPS on all large DBs to get them running as smooth as possible. You could also create a cluster and then just cut over when you want but that is a new post all together.