The key element to megawad's difficulty lies not only in level complexity, but also in huge number of interconnections between levels (a lot of levels could be entered and exited multiple ways). So instead of doing a simple walkthrough guide I decided to make a route layout with all interconnections between levels.
I recently started playing its successor, Junko and I remembered that I forgot to post the route guide here, so I'm doing it now.
Spoiler:You could download the resizeable vector version in the attachment.
Overall, while Crapi could be annoying sometimes (it has complex and confusing level layout, a lot of hitscanners, maps resetting on re-entry), it still was fun to play. My favorite levels were MAP21/MAP22.