So I have grown tired of seeing these things all over the place. I was curious if it would be possible to remove and plug them or just reroute them? Or will it make my engine run like crap? I would imagine that as long as there is vacuum in the system it wouldn't matter where the lines go. Or am I wrong?
It makes sense to take a more direct route than the factory setup. Most of the lines don't have to go under the plenum. One goes from the left side of the engine to the right side, to the trunk wall, ending up at the vapor canister - only about two feet from where it started. But for looks the factory way might be better. For the PVC connection you can use a loop of hose to replace the probably leaking, impossible to find OEM part. The guy who did the hybrid 2009 challenge hybrid Fiero just threw all that stuff out - and experienced problems. The PVC system keeps stuff from building up in your engine which can be a problem long term. Without the lines the computer probably can't even monitor the engine, let alone control it. Replacing rubber lines and tightening up other sources of vacuum leaks often solves a lot of pesky problems and results in a much better running engine.
You can re-route to please your eye, but everything still needs to be connected.
Here's what I did when I was refinishing my plenum and valve covers. I hated how they draped over the rear valve cover and ran along the rear trunk wall so I made my own lines with aluminum tubing from a hobby shop. I pretty much had to - I had no idea how fragile the stock lines were and they pretty much impoded in my hand when I was trying to remove them. PCV was also relocated to the front valve cover.