I understand your desire to head off as many "problems" as possible during construction, but I think it would be best to embrace the notion of build, then test, then adjust. I speak from experience here.
During construction I had 2 friends whose engine oil temps were lower than they wanted, even during mild temperatures so I thought I would head off that problem during the build and just install the louvered oil shutter. My thinking was that there was no real downside to having it. Well, from day one my problems were too much heat rather than not enough. In the process of trying to fix the problem, I wound up taking the oil shutters off because I realized that in the open position they still cut off some of the air flow across the cooling fins of the oil cooler and I needed all of cooling I could get. It still wasn't enough. I then resorted to installing a larger oil cooler, then installing two cowl flaps. Both oil temperature problems and cylinder temperature problems were fixed, but only after testing, getting lots of advice and implementing EVERY suggestion that implied I had screwed up the baffles and/or installation.
Every build is different. With all of the choices we have, we have to acknowledge that, even when done as well as humanly possible, the result of the choices will yield differences in performance, many of which are hard to predict until you test it. Both my friends who had too-cool running engines came over and helped address whatever faults they could think of with my installation. Ultimately, they acknowledged that on my plane, with my engine, ignition, compression ratio, nickel cylinders, etc, etc, etc, my plane ran much hotter than theirs.
Build to the best of your abilities. Then have lots of experienced eyes look for issues. Then test PROPERLY. Don't just fly off the hours. And folks who imply that you didn't build it right if you have problems just got lucky with their build or are forgetting or minimizing things they needed to address. Yes, use their suggestions to check if you in fact did screw up, but filter out the implications that "if it isn't perfect right out of the box, you suck as a builder".
You will also need to figure out both who knows what they're talking about AND does that advice work with my priorities. I have another friend who does stunningly beautiful work try to convince me that I needed to paint everything before initial assembly. He was speaking from experience in how to MOST EFFICIENTLY make an airplane beautiful. I ignored his advice because I knew that me building an airplane wasn't about efficiency in the build (7 years!) and also that I knew of planes with problems that should have been addressed but weren't because the owners didn't want to screw up the paint job. I didn't want to be that guy. Just embrace the concept that this is a hobby and is supposed to suck up all your time
In the case of cowl flaps, I don't see a downside to installing them during the build, except of course cost, weight and complexity but remember that I didn't see the downside of the oil shutter and wound up needing to remove it, so me not seeing too much of a downside should not give you much comfort
. I wound up installing them after I knew I had a problem and implemented every other suggestion on how to fix the problem.
And of course, I only discovered the effective solution AFTER the plane was painted