First of all, don't worry about blood clots. That is not what is causing pain in your knee.
Since you had this pain arise shortly after making a change on the bike, it is my guess that you've overdone things to the point of pain. The fact that both knees hurt at first suggests to me that the pillow you used caused your body to be in a position using the bike that was not good. I recommend that, when you use the bike, you stay with the adjustments that are possible on the machine itself. After all, it is designed to place your body in proper alignment when you exercise. Adding something like a pillow can mess with that alignment.
If you have access to an upright bike, it usually can be adjusted to give you a bit more challenge with the ROM. But quite honestly, you can do the same for your bend by placing one foot on a stair and leaning into your knee for a count of ten. You can do several reps of this bending 2-3 times a day and it will help stretch out the soft tissue. The advantage to this exercise is that you can do gentle stretching that should gradually increase your ROM.
As long as you're having pain like this, you need to ice, elevate and take something regularly to keep the pain levels down. Rest from exercising until it improves. It may take a week or so. More than likely, you have swelling going on in that knee and you need to get that taken care of.
I know it's difficult to imagine, but at five months you really are still in the middle of recovery. You aren't there yet. It's easy to overdo things and take a few steps backward. We all do it at one time or another. So don't feel bad about having it happen. Just scale back, take care of yourself and start again once the pain has lessened.
If for some reason your pain does not start improving in the next few days with lots of rest, icing and elevation....then you may want to give your surgeon a call so that he can check things out.