[Q] When did this series first air?
The first episode was aired in Japan in April 1988. The final episode was aired in March 1989.
[Q] Why does Ginrai look like Optimus Prime? Who is Devil Z? Is Black Zarak the same Zarak from The Headmasters?
The answers to these questions are never revealed in the actual series itself, but after the series finished an additional clip-show type of thing was broadcast which featured Shūta and Grand Maximus discussing various topics over clips of Masterforce and The Headmasters episodes.
This is the video you need to watch, uploaded by wutonchu, from 4.50 onwards. It explains the most frequently asked questions about the series although some of the answers just aren't that great (such as what Devil Z is) but it's the best you can get in terms of answers.
[Q] Where is everybody?
Masterforce was to be a fresh start for the Transformers, meaning that every character before this series does not appear in it, excluding Chromedome and Fotress Maximus.
[Q] Where were these Pretender guys during seasons 1- The Headmasters?
They probably found out that the other Autobots were under the leadership of Optimus Prime, so they decided to stay hidden.
[Q] Why do two of the Trainbots appear in the first intro?
I don't know. It's possible that originally, Masterforce may have been linked to the previous series more closely meaning that perhaps the Trainbots would have been used to transport Autobots from Earth to Athenia, since the space bridges had been destroyed, but this is just a theory. Nobody knows for sure.
[Q] Was there a manga for the series?
Yes. I've never read it but it does have some differences from the anime, such as different deaths for Giga and Mega, and Sixknight just being a member of the Autobots from day one. I've also read that Fortress Maximus appears in it and officially hands over leadership of the Autobots to Ginrai.