After spending enough time considering my options, I decided to go ahead and place my order for the engine and prop today before the April (Sun n Fun) sale from Vans expired. I'll be getting the non-certified Lycoming YIO-390-EXP119 with Dual Pmags, and Hartzell G2YR/N7605W-2X composite 2-bladed propeller with spinner.
I decided to get the regular non-certified and not get the Thunderbolt edition of the engine and save the extra $5k. Additionally, I didn't really want the ported exhausts because removing metal reduces wall thickness, probably reducing longevity, and makes eventual cylinder replacement more difficult to match later. I also don't care for custom paint colors nor chromed parts. Furthermore, I don't really feel that full assembly by a single person is a actually better thing than the assembly-line shift of workers doing single tasks.
As a side effect, the engine delivery timeframe will be much shorter (supposedly 6 months vs 18 months), though I'm not actually in any hurry to get the engine at this point. I'll have two years of warranty from when it's delivered or first runup in the plane anyways.