what is the perfect balance between weight/cost/function in the 11 speed di2 groupset (105/Ultegra/DA)?

It seems that the Ultegra shifter are identical to DA (button/reach) and you can save 20g with titanium aftermarket brackets.
The from mech seems to be DA/ultegra identical
The rear mech are internally identical DA/Ultegra (motor/gear) but the 50g difference?

12 speed maybe? I went for Ultegra derailleurs (better shifting and substantially less weight) and 105 levers+brakes (no benefits apart from hood buttons). As for the rest, aftermarket cranks and rotors are better than what you get from a full groupset. Dura ace chain (fastest) and cassette is a go to if you prefer hot waxing.

First of all, lol @ this frame. Not because it's bad, but because it's just kind of funny at how unoriginal these companies are getting. At least they are copying stuff we want.

I do feel like these offset seatpost frames require a rethink on how geometry is calculated. Most frames have a vertical BB offset. I think it's time to start counting horizontal BB offset from the seat post axis and rethinking stuff like STA, TTL, maybe even reach to be honest. Because where this geometry chart says your saddle is going to be and where it's actually gonna be are super different. I would not be surprised if we were talking about saddles being like 30-50mm more forward than the charts would indicate which obviously impacts fit, handling etc. Biggie is shortened effective reach. Other stuff like hip angle will be impacted too. So you would have to do another level of geometric analysis to truly transfer your fit 1:1. And it's possible the geometry of these offset seatpost frames will require a total rethink of fit.

True, although steeper STA should be accompanied with substantial increase in reach across all sizes to prevent sitting to far over handlebarsand excessive load on arms. So far, progressive geometry is still (and probably will be) a very niche stuff.

I'm in the final stages of putting together my order from LightCarbon and wanted to get your opinion before I pull the trigger.

My old bike was a Bergamont Grandurance RD7 in size 58, which actually fit me quite well. However, it was more of a commuter bike rather than a proper endurance bike.

I've now decided to go with the LCR-018D in size 54. For the handlebar, I'm planning to use a 400 x 100 mm setup (400 mm handlebar width / 100 mm stem).

A bit about me:

Height: 180 cm
Inseam: 82 cm
Shoulder width: 40 cm

My old bike also had a 400 mm handlebar with a 100 mm stem, which felt quite comfortable for me.

Do you think this setup makes sense for my measurements and the LCR-018D in size 54? I'd really appreciate hearing another opinion before I place the order.

Hard to tell how correct my assumption is, as I don't know you body measurements and lower threshold of comfortable fit, but this is very extreme size swap. If you are comfortable on Bergamont and want a bit racier feel, get size 56. Size 54 will require monstrous stem and a Jenga of spacers, or else you're gonna sit like a shrimp which will be neither fast nor comfortable.

Is it worth upgrading to an entry level carbon wheelset if I already have pretty light wheels? I wouldn't be saving much in weight but there's the aero benefits to consider. Would be interested in hearing any personal experiences.

As @dolph mentioned above it is totally worth it but also depends on how much you actually willing to spend. Ksyrium's cost is close to some good Elite/Tagoola wheelsets.

Is there a resource you guys recommend when looking at how to spec a wheelset? I've gone into the individual wheel threads and there seems to be lots of details and terms I'm not familiar with (rim width, spoke options, hub options, hub reliability, etc.).

It depends on what you want to have - custom built wheelset or comething ready to use? If latter, the budget-to mid segment is saturated with pretty decent options. Look for the complete build with steel spokes (pillar 1420 is a good starting point), DT Swiss clone (almost every brand has its 240 ratchet clone since the patent is void but skip hubs with excessively large number of ratchet teeth) and modern int/ext width (23/31 mm is the absolute minimum IMO). You will feel the biggest effect in regards of responsiveness (from carbon as a material) and rim width (superior grip, flat protection and cornering due to the bigger air volume inside of the rim).

I do not recommend custom build if you are not willing to geek up about hubs.

I tried my friend's FM316 size M (I am 180 cm, long legs). While I mostly liked how the bike felt on the road (need 10-20 mm extra reach) it feels smaller than I expected and when I go off-road it feels the weight distribution is off - too much pressure on the handlebar which may result in excessively nervous technical descends. The dilemma is, 420 fork will make the bike too relaxed and the 395 is way too low for me. The 405 fork from FM 346 should provide intermediate position with sufficient stack yet decent HTA that I really liked. Luckily, Jack was very cooperative and we made a deal for FM326 size L plus extra fork from FM346.
Will see how it plays out...

Does the wheel has pressure release channel?

Thanks! Have looked at the Speeder as well. But it has a rather racey geometry with low stack similar to my current bike so might not offer that different experience.
Thinking a bit about wheelbase as well, the System6 is super snappy and responsive, but also skittish on poor road surface of which we have a lot. Thinking a tad bit more wheelbase would make it slightly calmer.
Had a BMC Timemachine TT bike for a while and that thing was fast as f***k but also super planted on rough roads with bumps, cracks.etc.
Sports a slightly longer wheelbase as well as slacker steering angle, yet super aero,. Similar wheelbase and trail as the Lightcarbon LCR018 (but much shorter chainstays and longer front center).

Alright, I thought coming from SystemSix you wanted similar race feel that does not beat you... Than LCR018 may be a good choice for you. Nonethelss, I advise to read through the thread and note the (minor) issues people have with the frame set and decide for yourself if you are ok with it.
On the bigger brands side, you may check latest Giant Defy - it can clear 38 WAM tires, very comfy and fast. I often ride with a guy on this new Defy and he is really happy with it.