When you say "double the amount of traits" I assume you mean there are two of each trait rather than you are allowed to pick for traits to start.
If the former, you are using both the merged More Perks and the merged More Perks - DLC. Just use the DLC one.
As for "how many plugins this computer can handle", the mod limit is an engine bug not a hardware constraint.
Also @TJ, I was under the impression that all of the YUP content sourced from MM .93 was not included in the TTW bugfix. Is this not the case?