Is kapton suitable for use as high voltage insulation?
Kapton is not appropriate to wrap cables: it's relatively stiff, and thus won't be conformal to the cable, which leaves air gaps, which have lower insulation per mm. 

So, even multiple layers of heat shrink would be better.

At 5 kV, I'd start by trying to keep cables mechanically separated far enough that the air distance ensures sufficient isolation, even in the absence of any dedicated isolating material.

Use high-voltage cables, which come with the necessary isolation. Don't connect them at the same distance – cut one conductor shorter than the other, so that you don't break isolation in close vicinity.

There's isolating potting that you can use to fixate a solder joint.