When fighting trojans, hold down the shift key. I assume you know this but just saying.
When you hold it down auto-aim is on, when you're not it's off.
The Vile Striker line, is pretty good for FSC, and especially the mask phase, while doing well with trojans, and when you need some poisoning it's good as well.

Let's break them down.

The Snarble barb line, better for trojans during FSC, better for vanaduke's body phases, and decent for the mask, better charge, better
The Vile Striker line, not as good for trojans, not as good for vanadukes body phases, better for the mask, much worse charge.
The VS line is good against trojans and his body phase as well though, not as good as your DTB though.

Voltedge is probably the best of these three for slag guards. Charge up, dodge, release charge on their backs. Try that.

Overall, I'd keep the DTB.

Just my opinion from a not-so-good post.

I actually tend to take both into fsc together with my swordsman loads outs so I've seen first hand how they compared to one another directly. The BTB is much better throughout the citadel itself and I generally find myself only using my DVS on pierce-resistant enemies, although even then it's only especially useful for the Red Rovers and Blast Cubes, trying to DVS an Oiler is incredibly risky since you're liable to vault yourself into their oil and get lit up. Against vana himself DVS has a lot of utility for upping party dps and fills the all important roll of giving you a normal damage weapon for vana's mask. Both of them are useful in their own right, but BTB is a lot better over the entire course of fsc where as DVS fills a few key rolls which could be filled by most of other normal damaging swords such as the Calibur line.

Disregarding that particular more 'general' loadout discussion, for yours specifically you'll want the BTB because you lack any other form of piercing damage and the Voltedge will adequately handle anything pierce-resistant and is more than sufficent for vana's mask phase. Although I would highly suggest you drop the capacitor for a gun you can use to effectively dps vana such as Blitz Needle, since Polaris isn't exactly ideal for the job.

Hm. Do remember that you can use the arsenal, so there's no reason to give up the rapier for the entire run. I seem to always forget about the thing.

I'd advise binding autotarget to a key. I have problems with controlling rapiers too, and it helps immensely. Any time I switch to my BTB, I hold the key down and have no issues. Also, don't underestimate just how utterly piercing weps dominate things they're weak to. I find when doing the FSC, when you have a trojan on the field you try to kill it first and as fast as possible. As such, I'd stick with BTB for the run up levels.

Since nothing is weak to pierce vs Vana himself, the rapier isn't all that great. Switching it out for DVS would probably help on the mask. And there's really no reason you should be killing slag guards if you got someone with a shiver locking down Vana (which you should). Merely getting their aggro and keeping them away from allies is fine. Just kite them into the freezing field (but not into the freezer; I'll-- I mean they'll hate you forever if you do :p).