I'm with Matt on one6 but....
Mark is a good guy and he even drives an 8th gen tw coupe si. He did a good job on Matt's work and he had a nice clean install of the first turbo'd 8th I've seen in the Chicagoland area. last time I was at One6 Mark still did not have tuning capabilities but I know he could do your install.
I have also stopped by Suja and they were very friendly and helpful. I was asking about camshaft/pistons/pulleys/etc as well as tuning capabilities. They've tuned Honda's in the past but obviously our gen(I'm assuming you have an 8th gen) is limited at the moment. There shop has a couple built Honda's in the garage and one of the visits I saw another 8th gen on the lift. They'll show you some of their projects and you can judge for yourself.
Factory5: I think went out of buiseness but I could be mistaken.
GRD: These guys have tuned a lot of my friends cars, but they have been subaru's. They are a tuning shop so if you stop by I'm sure they'll talk to you and let me know if you do an how it goes. I've been meaning to stop by their new shop but I'm not ready for any real engine work at the moment.
Check them all out and speak with guys and ask if they've actually done bottom end work, pistons,rods etc.. on our gen or your gen. Good luck man, post up findings/results if you don't mind.
'07 SI Taffeta White coupe
AEM CAI, SS brake lines, Rota Torque (old bronze color) wrapped with Bridgestone Potenza REO1-R 245-front 225-rear, Stock Si rims painted black, 6000K HID's, 8th civic Chicago Crew sticker good for +20whp...