So let's see if I got this right:
Build 14 Beta 3.3, 9 Nov 2014: Performance is OK
Build 14 Beta 3.3, Plus NoLag update V1 (General Changes): Performance still at previous level
Build 14 Beta 3.3, Plus NoLag update V2 (As Above + Smuggling): Performance still at previous level
Build 14 Beta 3.3, Plus NoLag update V3 (As Above + Fetch Quests): Performance perhaps a little lower, but not sure of that
Build 14 Beta 3.3, Plus NoLag update V3 (As Above + SeaAI): Performance still at previous level
Build 14 Beta 3.3, Plus NoLag update V3 (As Above + Perks): Performance dropped down to Beta 3.4 level
Build 14 Beta 3.3, Somewhere January: Performance was BETTER than any other version mentioned here
Build 14 Beta 3.4, 19 Jan 2014: Performance is notably bad
To clarify, when you installed the SeaAI and Perks updates, did you do that on the NoLag V3 version or on the original Beta 3.3 you posted?
It was intended to be installed on NoLag V3, so if you installed the Perks on Beta 3.3 without it, that may not work as it should.
Basically Build 14 Beta 3.3 + NoLag update V3 + SeaAI + Perks should pretty much be equal to Beta 3.4 (minus your own settings tweaks).
So what happens if you install ALL of those and compare it to Beta 3.4?
Technically there should be no more difference: Functionality should be the same and performance should be equally bad.
Exception is the shipyard lag, because I did still exclude that.
Can you also please try the latest Beta 3.5 WIP? It seems the Perks are the most likely cause of this, but the WIP contains some further changes to that.
So I'd like to know if those changes made any difference at all, for better or worse.
Also, I don't see how a January pre-Beta 3.4 release could have better performance than ANY other version.
Basically the NoLag update series should have covered that stage.
And Beta 3.4 was released on 19 January, so the BEST version would have been REALLY close to the WORST in timing.