1- FCMing your existing MSN-MSP-EWR will get you 150% MQM on those flights; since you will then have a ticket booked in A, you will be able to SDC to alternate flights (possibly via an alternate routing) where FC seats are available
2- once you're inside the 24-hr window, you will see a "change flights" button on the OLCI page; clicking that button will bring up alternate flights, and will identify the cost (if any) to change ... since you're thinking about adding a connection, there will probably be a small additional charge for segment fees/taxes/etc ... note however that when I tried this on Wed afternoon, the system did NOT show me the later Thurs flight that I wanted because it was still more than 24 hrs until that one departed; at that point I called and had no issues with the PM line agent processing the SDC
3- if the alternate flights you want aren't offered, it may be due to routing rules; there's nothing to say that you couldn't get an agent to process it ... you might also be able to SDC the MSP-EWR portion to MSP-ATL-EWR when you're at MSP