ok so here is what i would do if i was to keep that piping design.
Remove the pipe, weld in a patch panel of 0.9mm body steel, from the underside of the chassis. Then make a new hole for the piping around 3.5" and slightly forward as it seems to be rubbing on the front section. test fit to make sure all is smooth and no fouling.
Then, i would paint both sides of the patch with an etch primer then some chassis black paint.
get some cardboard and trace out a piece that will cover the battery tray right the way under the guard mount, all the way to the wheel well and back to the chassis rail towards the centre of the car.
Use that piece to cut out a Flat sheet of 2mm polished alloy so you can cover the entire area. mount that with screws into teh old tray. then you can cut a matching hole in that from underneath to match the bottom hole.
use that alloy sheet to remount those wires, install a catch can, radiator over flow.... etc etc etc
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If you want it done as cheap as possible, you could follow the above, then cut out your patch panel and the patch, needs to me no more than 1mm gap all around, then just take it somewhere to get tig welded up, might cost you $50 to weld it depending on how good your cutting and patch is.