Great to hear you're getting everything worked out. My valves were also noticeably louder after I installed stronger valve springs.
Hopefully you have better luck with the hypersingle. If you need a transmission, let me know since I'm selling mine with a FRPP torsen diff and 4.06 gear.So next week ill be pulling the trans and replacing the clutch. Also look into the the 2nd gear shifting issue. Talking to Terry Haines, he seems to thinks its either a shift tower issue or misalignment with the shifter cables. Stay tuned.