I guess no one else feels like answering this.
For the higher compression without resleeving the block, jdm type-s pistons are your only options. Our FRM sleeves don't take well to forged pistons. Check the condition of your cylinder walls when you pull the head to see if you need to hone them. Or just buy the .25 over, type s rebuild pistons and oem rings, and bore and hone the cylinders to match.
The thinner head gasket wont bring you much closer to 12:1.
Crower valve train components would be good. The Skunk 2 valve springs have been too stiff for some people's valve train, resulting in scored rockers over time.
Your greddy header is fine. If you end up going with the SMSP, definetly get the custom exhaust piping to match. (SMSP header moves the cat location further back)
Intake manifolds, forget about the Skunk2. And you can run an extrude honed euro r manifold if you're ready to do the modifications to it that are necessary. I'd just send your current intake manifold to portflow and have it ported & matched to your head when they work on it.
Engine management, you've got AEM EMS or Hondata. Just remember that you're going to spend quite a bit of $$ on dyno tuning either system. (I dunno about you, but dyno tuning here is pretty expensive.)
Good luck with your project.

I wish I had a second mode of transportation so that I could get working on mine already.