I'm a low

kind of guy, so take this for what it's worth. I wasn't committed to completely removing the plenum and doing everything you are going to do...I was just trying to find an alternative route to the PHH. It turns out it was just as easy to go in from underneath because the only way I could see to get to the PHH from above was to remove the lower part of the manifold as well. Everything else I did was a side effect of the PHH. It just kind of grew out of control.
If I had to do it again I think I could do it pretty quickly. It only took me about 20 minutes to reinstall it. I ended up with two extra bolts from the whole project (starter, intake plenum, removal of the air filter can, PHH, valve cover), but for the life of me I can't find anyplace that is missing a bolt. The thing I had a hard time with was where the EGR modulator (I think) attaches to a large pipe that disappears by the firewall towards the bell housing. I think it was a 22mm nut, and even after it was loose the EGR didn't want to move. It was THE hang up to getting the whole plenum to move. It was easiest to reach after removing the air filter canister and standing in that area, leaned over the engine. Others have recommended spanning a board across the fenders to kneel on and removing the hood for more access. Whatever works for you I guess.
A couple of things I found critical to the whole thing:
1) A good magnetic pick up tool. I have one that is rigid and about 8-10 inches long. Very good for placing and recovering bolts.
2) Autozone sells a socket extension that is a flexible spring. I got the 1/4 inch and the 3/8 inch. These were great for the valve cover bolt by the firewall and some of the plenum bolts. Using the extension to tighten the valve cover bolts gave it just about the right torque (finally!)
3) 2-3 feet worth of socket extension to get to the bolts under the plenum.
4) On the PHH, I finally gave up on trying to fit it back together with the pipe that runs between the engine and the firewall. I routed a heater hose all the way using springs on the bends to keep it from collapsing/kinking. If someone can convince me the pipe is the only way to go, I still have it in there and would consider fighting with it again. I did use the clamp from 1fzfephh.com though, and I kept the short section of gates hose that came with it. I would recommend just picking up the replacement hose while you are getting all your other parts. If you end up swearing at the thing at 1 o'clock in the morning you can just short cut by bypassing the pipe until you have forgotten the misery and want to give it another go...just like having kids. That's why they are at least 2 years apart. If you don't use it you always have the receipt.
PHH tool 1) Linoleum knife from home depot
PHH tool 2) Small vice grips for removing the clamp with the ears facing the firewall
5) I was stressed about all the different vacuum hoses that go everywhere. Really, it wasn't too hard to figure it all out again. Except for the small hoses under the plenum and on the EGR, most things only fit in one place. I took a lot of pictures as I went because I was doing it in my spare time over a couple of weeks and didn't want to forget where everything goes. They helped.
6) There is a great thread on removing and reinstalling all cables related to the throttle. Read it carefully and going back together will be much less stressful. Take note of what "good" looks like on all your gauges BEFORE you do any of this service and getting back to good will be easier.
7) Ratcheting box wrenches. Size: 12mm (2 each), 10 mm, and 14 mm.
8) Nice to have: A 3/8 ratchet with a t-handle on the end for quickly spinning the bolts once they are loose. I got it at Harbor freight, but I don't see it in their online catalog now.
9) I used my air compressor to blow out hoses, pipes, blow debris off before removing valve cover, etc.
Good luck!