I passed through along the PAN AM highway about 2 months ago.
Budget and concerns about security meant I stuck to the route and passed through El Salvador, Honduras and Nicaragua fairly quickly.
I can't say anything about the routes you are choosing, but to add to the other commenter, I never had problems with the people.
They were generally courteous and curious about my travels.
I never felt unsafe or uncomfortable except at one border crossing into Honduras where too many people were jostling to help me even though I didn't need it.
Even that was more over enthusiasm by the people rather than intimidating behaviour.
The PanAM is generally very good. Well paved with some sections with bad potholes that would not really worry a cyclist.
There are a few big hills but no really major challenges from what I remember.
I stayed in hotels every night. They are relatively cheap and was the only secure option along my route.
My credit card worked in all the cash machines without problems.
The worst thing for me was the heat.
Resources are limited so food and water are in short supply especially in south east El Salvador and Honduras. (and later on in Panama too)
Make sure you have snacks and water with you.
The bigger towns have all the usual options for evening meals and breakfast though.
I'm sure I don't need to reiterate the comments on security. Keep your stuff away from prying eyes.
I was advised by locals and police to stay indoors after dark, and having seen the news from El Salvador AFTER I left, It is probably good advice.
Again, from what I was told the gangs fight amongst themselves or the Police and generally do not target tourists or cyclist.
Just be sensible.
Apart from the extreme heat, I actually enjoyed travelling along this route
I'm sure you will too.
My blog notes are here if you are interested in reading? http://theroadoflittlemiracles.ghost.io/0051/