In my opinion the modified cover covers the only part of the gen 3 that doesn't need dressing up... The plumbing, wiring, and coils on the heads looks atrocious while the intake manifold is simple and "not unattractive"

I would definitely encourage you to make up something to dress them up if possible, no matter what you do with the stock cover.

That being said, the body may help hide them somewhat as well...