With bare IPsec (i.e. no L2TP/IPsec or another kind of tunnel whose transport packets are ciphered using IPsec), there is no interface to set MTU at, but on a simple site-to-site IPsec link, PMTUD should work fine unless a firewall at one of the ends of the tunnel is misconfigured and blocks ICMP "fragmentation needed" messages. If you do not experience failing connections via the tunnel, it means that PMTUD works fine and you don't need to care about the MTU.
Regarding speed, the IPsec payload traffic must indeed be exempted from fasttracking as one of packet processing steps that most (not all) fasttracked packets bypass is the IPsec policy matching. Since disabling fasttracking completely hasn't helped to reach the desired speed, there must be some other limitation. Not all Mikrotik routers support IPsec encryption and decryption in hardware, and even those that do only support a particular set of algorithms (details
here). So what is your uplink bandwidth for upload and download, what is your Mikrotik model, and what is the speed through the IPsec link?