The power loss is puzzling, I must say. I have a hard time coming up with anything. Your thigh-torso angle is not too tight, IMO. Did you try the lower saddle? Your elbows are a little far from your knees. Does it feel any better to pull your elbows back (just guessing here)?
All I can guess is that the neck and shoulder thing is really bugging you and inhibiting your riding.
Thinking back, I first made my change to a lower aero position during a time that I was doing trainer rides twice a week. I would do the warmup and rest breaks sitting up, and get down in the bars intermittently during the intervals. Like, do a 15-minute interval as 5 minutes sitting up, 5 minutes down, 5 minutes up; then switch the order for the next one. As I worked up to spending the full 15 minutes down, I put a 6" block under the front wheel. This ensured that I was holding the right joint angles, but took weight off my arms and shoulders while I adapted.
By the time I went out for the first long rides, I could stay in the bars easily. I think the short hard intervals in the bars, with rest breaks, really helped me feel comfortable at normal endurance power levels.
Try some trainer rides with the front wheel raised 6-8". That might feel better in the bars and give you a break while you adapt. I like controlled situations when trying something new.
Yes, I did try lowering the saddle. I overdid it at first (down .75cm, which made it feel like I was riding a tricycle), then reduced it to about .3cm lower than at the start. Seems OK now that I’m more used to it. My low back felt better and saddle pain was reduced, but that could also just be from more riding. I’ll re-shoot some pics soon.
RE: elbow position, I actually find myself preferring to be more stretched out. I spend more time with my hands resting way out over the shift levers. Now, when a rise in the road comes along, I slide my hands back and my elbows come very close to touching my knees. I move around so much that it’s hard to say what’s “best.”
As for the power loss, I’ve ridden the trainer 2x, for interval sessions. I simply can’t hold the same watts as on my road bike (20-35w less). I alternated between road and aero bike, just to make sure I wasn’t tired or something. Nope. I have 2 trainer sessions planned this week, and with only 5 weeks to race date, I’m actually starting to become reluctant to invest any more time on the aero bike – I may be racing on my road bike w/ aero bars instead (gasp!). I may use your suggestion and jack up the front as a test.
I have another example of power. There’s a 7 minute climb I do on virtually every local outdoor ride. I’ll slowly build power up it and over the last minute or so hit max effort. I nearly always finish those final 20-30 seconds in the 400w+ range on my road bike. On the aero bike… barely 360w.
As I ride aero, I notice that if I pop up onto the Hed bar’s “hoods”, RPE suddenly drops and/or watts go up. I’ll cruise along at watts that match the RPE of my road bike again. Could be comfort, could be that I’m just stronger with a more open hip angle. Either way, it sucks!