Hey champ, to answers some of yours Q's.
1.Yes running an oil catch can is fine, some will disagree and some will agree, and no it will not harm your motor. If this were the case, 90% of modified engines would fail, so it's fine. Mine has run one for years and has not had a problem.
2.I've seen a few now with these lines bypassed, as apparently more power is meant to be made due to the fact there's no coolant running through plenum. Dyno results have shown no power increase, so it seems pointless.
3.I personally wouldn't purchase an e-bay clutch(cheapy) as i've known of major failures. Save your bikkies and buy a decent, well known item. As clutches are a weak point already from factory, and most the e-bay ones look and sound promising, but most look crappy and cheap. The exedy HD is a good kit.
4.With headers, and this may open a can of worms. It's very difficult to gain any hp with an aftermarket header with a STANDARD engine. Yes there's gains if you go all out on an N/A monster. But in standard trim, honda did an unreal job and in many cases you'll lose power rather than gain. Also be careful of some of the e-bay systems look identical to the factory ones, only polished with worse bends. I don't think there are any good cheap off the shelf exhausts. If you do choose to go custom, keep it single outlet 65mm pipe with minimal bends.