Excellent idea! But I would like pool work for tempo instead of bike riding.
As for speed work, yes the theory says that healthy individuals must not get too far from speed work yet, this is not your case. Remember that every sprint session must be somewhat slightly better than the last, you’re not getting better, you’re getting worst, THIS IS NOT THE GOAL OF PROPER TRAINING.
As for Hams, have a therapist or yourself doing soft tissues work there, It is not like you would be able to run without you hamstrings…
For the knee, It is often the result of trigger point in the rectus femoris muscle, happen to me also each time I don’t get enough recovery, do trigger point and It works like magic (If the knee issue Is because of that)