Most vacuum lines are tucked behind or under the intake, so I can't see how they can be considered clutter. If you think they're ugly, try some cool covers for them or something.
To answer the original question, I would say that the line going to the tree on the firewall is necessary. That goes to your HVAC system and brakes.
Another one that is necessary is the one that goes from the intake to the fuel pressure regulator.
If you've eliminated the EGR and air pump, you don't need the line going to that tree that sits to the passenger side of the engine.
I think PCV is important, so the line to the PCV valve should stay (It's under the intake anyway) and the one from the throttle body to valve cover should stay.
If you have an evaporative emissions canister, you should probably keep that line so that the canister doesn't get filled. If you don't have it, you'll think you have a fuel leak all the time.
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351W 89 Mustang GT Convertible