I hear you. I went out and did a whopping 9 miles on my bike yesterday. Averaged 18.5 mph in my hilly little area of the world. Not too far off what I was doing last year. Today I am feeling it in my ###, lower back. and hip flexors. I went out for a little run after (4 miles). Felt great for 2 miles (7:30s), then my body said "I'm done" and I limped in a 9min/mile for the last two.
I think there is a bike fitness issue here, somewhere.
Mine is a strength, not stamina issue. I need to get on my lunges, and start putting some "fast" miles in. I would normally try to build a base right about now, but I'm in fairly strong cardiovascular shape, but am having trouble with speed. I'm fairly certain that training for my ultra had a lot to do with it = too many slow miles with little to no speed work. I usually can get myself into bike shape fairly quickly, but as I'm getting older, getting running speed back that is lost is taking quite a bit longer. I'd really like to be competitive in the duathlon that I did early last April, but I currently have less than 6 weeks to train for it. Yesterday was my first bike ride outside for the year, and my running times have been waaaaay slow. My last year times and ranks for the race were:1st 5k: 21:08 (6:49 pace = first in divison)
T1

51 = first in division)

I nailed it!!
Bike: 34:59 (20.6 MPH= 2nd in division)

missed a turn which cost me, and like this year, wasn't bike ready
T2: :49 (= 3rd in division) lost a couple seconds here as my bike fell when I tried to hang it
2nd 5k: 22:09 (7:09 pace = 3rd in division)
I took 2nd in my age group (40-49) out of 11 (missed first by less than 2 seconds); and 4th out of 79 overall.
Right now, I'm not even doing 1 mile intervals @ 7:09 pace, and can't realistically expect to get near 7:00 pace for either of the 5k's. I'm writing goals down now, as I really want to do this race, but won't do it if I can't get faster (= hopefully, writing goals down now will help me get there). Here's a shot at what I think are reasonable, but pushing it goals:
1st 5k: 7:15 pace (= I'll be approx. 1:30 behind last year)
T1: :55 (can't expect to nail it again) = 1:34 behind
Bike: 21.8 MPH (= 33:00) it is an awful course for time, with multiple hard turns and bad pavement = ahead :33
T2: :45 = :37 ahead of last year.
2nd 5k: 7:20 pace = almost identical time to last year.
I will also be starting closer to the back of the pack, as I want to start AFTER the person who beat me at the line last year for first in our division. I knew that he had started behind me, and during our sprint to the line, I knew even tying him would have me in second = he nudged by me at the finish (running a 20:56 5k) and won by almost 2 seconds (the difference at the start).
I have a half marathon next weekend, which I will not be racing, just running. After that I'll take 5 weeks of speed training to see how much quicker I can get.