Regarding shaping and queuing you may find useful to have a look at FQ_Codel and Mikrotik CCR CPU Utilization and some quick comments on configuring cake topics if you haven’t already. Although this does require moving on to v7 (preferably with Netinstall than building up the configuration from scratch to match the new methodology).
Another thing that you may want to look at is to move on from PPPoE to DHCP in order to solve the issue (if your accounting system supports it).