Not much you can do through config to improve link rates once you've reduced the number of SSIDs per AP in use ("beacon pollution"), eliminated the legacy and slower rates, and reasonably prevented same-channel interference. You could remove some of the slower base rates, but that might mean that weak-signal stations wouldn't be able to connect at all.
On your 5 GHz setup, at least in the US, channels 52-144 may be impacted by DFS. If DFS kicks in (and it is illegal to disable it in the US and many other jurisdictions), the AP might shift to a non-DFS channel, causing same-channel interference. You might try configuring 80-MHz wide on only 36 and 149, depending on the separation of the APs. With lower range on 5 GHz, there might not be significant AP-AP interference. You could also try 40 MHz channels on 36, 44, 149, and 157 (assuming you are in the US). There's a good illustration of the 802.11ac bands at http://www.revolutionwifi.net/revolutionwifi/2013/03/80211ac-channel-planning.html