I'm not sure if you're running a WISP, but this MUM presentation I did will probably be helpful.
Essentially you need to set MTU in 3 places:
L2MTU on the interface
MTU (which is Layer 3) on the interface or VLAN - This is 1500 by default which is fine for VPLS but if you want to test larger packets with the DF bit set using the ping command, then it needs to be raised.
MPLS MTU
The other two MTU settings you mentioned are likely:
VPLS MTU
Bridge MTU
Unless you need to pass an L2 frame larger than 1500 inside of the VPLS tunnel, then you don't need to modify these
Here are the minimum values for MPLS with and without VLAN tags
The MUM preso is here:
https://mum.mikrotik.com/presentations/ ... 279781.pdf