Have not read all the posts so sorry if I repeat anything. So long as nothing medical wrong (sounds like it has been investigated) it may be you have been working at a to much for to long (easy to do on a bike) and may well just not getting enough recovery. Problem with to much work/intensity is you can manage for so long (sometime couple of years)then it suddenly hits you.
Also sounds like you could prioritise speed a lot more as has massive impact on recovery (at least 8 hours, possibly more is often required if active, which you are)
If your interested check out ‘phil maffetone’ he has some great info for heart rate training and importance of not working at a to high rate for prolong periods which is what a lot of people do, has loads of other great stuff which might help as well.
I use his formula to calculate my max aerobic heart rate (for me it is less than 139) I stick to it or less when commuting and it has made a big difference in preventing me from getting to tired, basically stops me working to hard to often.
Another great place to look is a book: primal endurance by Mark Scisson, again some great info, although more geared towards competition.
Again as others have said it might be worth taken a decent break, maybe at least 4 week of and see how you feel. If feeling better slowly build back up again
Anyway, hope you find something that helps resolve your problem.