how do I manually save a rich text format document along with images as PDF?

Most applications give the option to export or print to PDF format.

What app did you use to create the document?

You are using El Capitan, and Pages. Since no release of Pages v5 supports RTF/RTFD documents, you may be using Pages '08 v3.0.3, or Pages '09 v4.3 — either version is advised for best El Capitan compatibility.The latter opens and exports RTF and RTFD documents to PDF just fine on my El Capitan 10.11.4 machine.

If your Pages '09 is not v4.3, and it was originally installed from an iWork '09 DVD, then you should apply the last Apple update for it — Apple iWork 9.3 updater. This update was not available to you on Snow Leopard. It will give you versions, and autosave in Pages, and quite possibly better behaved software.

Save and restart your computer. In pages you can save the document as PDF, but you can also Print it, as Lannyexplained. You can also export it as PDF after opening it Preview.

Does the document saved in Pages native format look OK when you relaunch it? When you open it in Preview?

Also, check your page settings in Pages and the Print dialog to make sure they match.

mac mail - I do a monthly Newsletter that I compose as an email & then convert it to RTDF & then to PDF

Not clear on your workflow. What are using to create the document? And why are you saving it as a RTF document when it can be saved to a PDF directly?

I've seen other reports here that PDF printing is broken in Mail. You can search for the discussions, but I don't remember reading about a solution.

As a temporary work-around, copy the email contents from Mail and paste into a blank Pages document.

Report to Apple here: http://www.apple.com/feedback/

Interesting, it has always worked for me. See example below:

Pages documents just saved as a PDF.

When you use the Print option, Command-P, there should be an option to save as a PDF.

What application were using for the RTF document?