I think it's the traits that need nerfing more than the chaingun itself.
I would suggest Reducing SoaB to 2 levels and making TH either only +1 bullet or only 1 level.
Also, Plasma Rifle is also very overpowered compared to its' late-game peers , the Double Shotty and the Rocket Launcher, for the same reasons. This was addressed by myself
here. Also note that the fact that SoaB damage is armor piercing is more important in the late game. Nerfing traits would compensate for both weapons.
IIRC, Modular has SoaB much less effective than it actually is: I believe that it gives +1 AP damage, not on extra side on the dice. I may be wrong, if so correct me, but if I'm right the chart should look like this:
On non-armored foes:
NT: [(1d6)]x5 17.5 damage
SoB1: [(1d6)+1]x5 22.5 damage
SoB2: [(1d6)+2]x5 27.5 damage
TH1: [(1d6)+2]x7 38.5 damage
TH2: [(1d6)+2]x9 49.5 damage
SoB3: [(1d6)+3]x9 58.5 damage
About a 225% increase. (Don't have a Calculator handy)
On armor level 2 foes:
NT: 10 damage
SoB1: 13.33 damage
SoB2: 17.5 damage
TH1: 24.5 damage
TH2: 31.5 damage
SoB3: 40.5 damage
305% increase
Anyway, implementing my suggestions would reduce the final damages to 38.5 and 24.5 respectively-120% and 145% increases over the base damage. That's a quite a drop from 225% and 305%- nearly half and over half respectively.
Of course, a 120-145% damage increase is still absolutely ludicrous IMO for spending 3 traits. Therefore, I'd still recommend increasing the effectiveness of shotguns as well to counter. Remember, even without these traits chain weapons were still much more commonly taken than shotguns- and shotguns require three traits, two of which are useless filler, in order to even be usable in the first place. Your call on that though.