I'd say the very first thing you need to do, before anything else, is work out exactly what he's going to be rules-wise in the army; then
start thinking what to do to him to make him 40Kified. That way you'll have a much firmer grounding in how to go about converting him up and in what gear he'll need to represent whatever-it-is decently.
A Shaggoth is so big that I'm thinking he's going to work best as something on the order of a Daemon Prince or a Defiler/Soulgrinder. For either, here are a few possible ways to go that spring to mind:
• replace the two small arms with servo-arm type mechanical pieces, or at least add in so much guitar wire as cabling that the existing arms look augmetic
• the model's own axe is way
too medieval-looking; replace that with a bulky power weapon of some kind
• add armour pieces around the legs, something like overlapping pieces of plate would fit the form of the legs best and still fit with 40K armour patterns
• the face would work well with more guitar wire added in for augmetics; think of this Angron pic as a guide:
...that might also be good guide for his hair. The long flowing locks are all well and good, but they're a bit Timotei for the GrimDark...