This is how I installed an aftermarket Mustang 2v plenum on my '05, I am pretty confident it can be improved upon but this is a start.
What you will need to do it this way:
- New plenum(duh)
- hose clamps(4 will be enough)
- 1 1/2 feet of 3/8" vacuum hose or other hose that will hold up(I used fuel line)
- 1 1/2 feet of 1/2" vacuum hose or other hose that will hold up(I used fuel line), I tried heater hose and it just collapsed under vacuum.
- Heat gun(to remove factory connectors from hoses)

If you look at the '05+ stock plenum you'll see it's basically the same as earlier models except that the throttle cable mount isn't tapped and the same for the IAC valve mount, it's also not drilled through.

So I went and picked up an Accufab plenum and looked at it, didn't take long to figure out what I was going to do if it would work.

The connection for the PCV hose is a tube that's the same size as the opening for the IAC valve. The only hard part was getting the PCV connector out of the old plenum, PB plaster allowed it to basically twist out.

I removed the PCV connector from my old plenum and fastened it to the Accufab plenum in the IAC port.

This is the original PCV hose which will not reach the new location on the opposite side of the plenum, you will need those connectors though. I used a heat gun to warm the ends and the connectors were able to be pulled out.

The front side of the Accufab(and other Mustang plenums) has one vacuum connection that I just turned around and used for the vacuum lines going into the EGR valve.

The backside(windshield side) of the plenum has 2 vacuum ports that match up with the ones on the original(brake booster and EVAP purge valve). I had to lengthen the line for the EVAP purge valve so I used 3/8" fuel line and the factory connector for attaching to the valve(a hose clamp holding the hose and the connector together), a hose clamp on the plenum. The clip on the plenum end of the factory hose will be extra since it doesn't clip onto the new plenum.

For the PCV vacuum connection, I used 1/2" fuel line and the 2 factory connectors, the connectors are held by hose clamps just to make sure they don't come apart.

Front side installed:

EGR vacuum connections:

Back side:

It was a good compliment to the 75mm BBK TB I put on earlier this year.