Are you sure you don’t have a MTU size problem?
If I see correctly.. are you configuring the ethernet ports on a fixed speed? Normally you should not do that. It can cause a duplex mismatch.
Fragmentation and duplex mismatches are a disaster for speed.
How many sessions does your torrent client have open?
At a glance I see rate-selection=legacy in wireless data rates
and
authentication-types=wpa2-psk in wireless security profiles.
Try data rate advanced and aes encryption.
Check your PPPoE client settings and MSS according to this article:
http://wiki.mikrotik.com/wiki/Manual:RouterOS_FAQ#TCP.2FIP_Related_Questions
HTH,