Cold air intake

There should always be clearance as the motor moves and shift around, you may eventually wear a hole through it and that would essentially be a vacuum leak. When you say the top of the engine bay where exactly do you mean?

Hope this picture helps

It does. You should be able to loosen the clamps on the couplers and shift/turn the tubing a bit to gain clearance, if not you could use a square of black duct tape there and replace it periodically. What exactly is that plastic piece its rubbing on? Is that part of the original intake?

Here

Oh its the intake manifold, that could be an issue. Like I said previously, loosen the clamps and try to shift it around a little, if that doesn't work you could make a small bracket that goes from the bolt on a clamp to something to keep it away from the intake manifold. Probably wouldn't hurt to replace your motor mounts either to prevent some flex, they should be pretty easy to change on that

How isthis

It looks like you're good to roll! Lol. Just to be on the safe side you could put a small piece of tape on the pipe and check it in a couple days to make sure its not making contact as things move and flex, looks like you nailed it though good job!

What type of tape

Masking tape would work well and you could even use a black marker to comoflauge it