You're in good company. I did the 3800sc swap and added WCF headers. 86SE4spd. Same situation as you. Verrrrry tight situation. I needed heat shielding so I used the 3800 heat shielding and modified them. Actually I grabbed an extra pair at the pick-n-pull giving me 4 total to work with.
I did the cut, nip & tuck routine to cover each runner and some I had to secure using stainless steel tie straps. It's no prize to look at but it's in a location that's hard to see.
The rear header at the trunk was easier plus I added an upper shield above the header out of sheet metal to protect the inner side of the deck lid.
I thought about adding Heat Shield Sound Deadener Insulation to the underside of the deck lid to protect the paint on the surface more so than reducing the sound level. Another fabrication job.
You may be better off rerouting and extending the harness in a different direction.
Spoon
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"Kilgore Trout once wrote a short story which was a dialogue between two pieces of yeast. They were discussing the possible purposes of life as they ate sugar and suffocated in their own excrement. Because of their limited intelligence, they never came close to guessing that they were making champagne." - Kurt Vonnegut