Multiple Instances in AlwaysOn Availability Groups - Resource Balancing
I am already working on a solution to re-balance the resources in the event of a failover, so no need to account for that in your reply.

That's actually the main thing that drives the reply.  If you don't sharply limit each primary instance it will acquire an unfair share of the server memory, and you may have severely degraded performance of the other instance after failover.
If you rebalance by setting max server memory for both instances in the case of a failover, you may run without limiting it on each node normally.
I would not limit the CPU affinity or maxdop on either instance.  The OS allocates CPU resources very dynamically and fairly, so unless you observe one isntance being starved by excessive CPU utilization from the other instance, just leave those at the default settings.