The semi oil has been in since the new top end was installed. It has been in through the heat cycles and dyno break in, and dyno runs. I assume the rings are seated, but also assume the engine hasn't been fully broken in yet. It has about 200 miles on the build so far I think. Before I ride it anymore, I'll be doing an oil change with mineral oil, and after 2500 miles, I'll switch to whatever oil at that point, as you suggested.
The lifters are S&S, and were put in only about 2000 miles ago, along with the cam chain tensioner. Dave thinks it's valve noise, or maybe just the TB noise. I figure the only thing I have control over trying is adjusting the push rods a bit, so my mechanic is going to check out the adjustment. He will also replace the O2 sensors, and check the torque on the header flanges.
It's not a horrible loud noise, and it's not a ticking sound. It's hard to describe- before I could just hear the valvetrain very faintly in the background, but now it's way more noticeable. Like I said, I'm sure part of it is with the quieter mufflers I can hear more of the engine. The sound isn't alarming like something is horribly wrong. I'm guessing and hoping the push rod adjustment will do the trick.
Numbers wise, from what I recall from the charts you have posted, your 113 build with headwork and 58 mm TB averages around 128-130 squared, so numbers wise, I think it's on par give or take a few.
Mechanic is coming by Friday night, so fingers crossed.