Remember that I am building this strictly for fighting Borg. I tend to get killed by the Tractor Beam then Torpedo/Cutting beam raping which is all Kinetic from what I understand.
Tractor Beam, Torps, and the Cutting Beam all deal Kinetic damage, yes. Your shields have 75% Kinetic Damage resistance, so other than the 10% Bleedthrough (or 5% with Resilient Shields) you shouldn't have a problem if you can keep your shields up.
Given that he has 3 DHCs, 3 Turrets, and a fore torpedo launcher, with this layout I would prefer having two CSV and two APBs with a TS.
Two CSVs with two APBs allow you to debuff entire groups constantly, which you can then take advantage of with a torp spread. You lose out slightly on single target DPS, but you'll do much better against groups - plus CSV will take out High Yield Plasma torps from the Borg. You also contribute more than just your DPS, since you'll be increasing the damage everyone else deals as well.
I'd also stick EPtS1 on the Ensign Universal for 100% EPtS1 up time. You already have a hull heal from HE1 and Aux2SIF1, so having stronger shields is a good idea, especially since it's your primary defense against Kinetic damage.
When I flew a Chimera I actually went with a LtCdr Engineer, which allowed for two copies of EPtW1 and EPtS2 along with Aux2SIF2. However I was running all cannons with no torps, so the EPtW1 helped. Only did around 5k damage, but I ended up being the tank a lot of the time, even with 0 ranks in Threat Control.