As a native speaker, I would say those sentences could be totally fine for Chinese to understand. However, the position of 了 could change the focus of your sentence slightly.
1.
昨天我骑了自行车去书店。
The first sentence is correct if you want to slightly emphasize you rode the bike to the bookstore.
昨天我骑自行车去书店了。
However, the correct version is better if you want to slightly emphasize you went to the bookstore by bike.
2.
他感冒了,昨天我去了看他。
We would barely use this sentence if we want to express "He was ill, and I went to see him yesterday." Instead, we sometimes use 他感冒了,昨天我去看了他, and sometimes use 他感冒了,昨天我去看他了。
These two expressions have no difference in meaning.