Hi
I did the same migration couple of months ago.
I installed the new version SP4 in new directory on both machines, and configured to run in different port say 589.
Created another two replication from the existing MMR to the new one but one way. You can do both if you are confident that nothing will be changed in the new instance.
Once the new instance is populated with new data shutdown one of the sp3 instance with 389 port. and immediately change the port number in sp4 instance 589 to 389 and start the instance. Please note: you have to make this changes in MMR configuration as well.
I will wait for a day and observe any problem and then do the same to the another instance.
The steps may seem convoluted, but it is riskless and no downtime.
cheers