First on my list of problems: can I make it so that the entire map is a Custom UFO and if so how?
A UFO by definition (at least mine) does not occupy the entire map, as normally it is not a perfect square, and even if it was, you need to put south and eastern external walls outside. So no, you need to at least place the ground underneath it.
But if you mean the whole area being a single terrain block (map), then sure, you can do that. Just remember to include spawns for X-Com units.
Second: is it possible to recreate UFO extender's Wreck Analysis via missionCompleteText (or any of the other types of text like that) and if so how can I
I don't know what this option did, but I assume it gave you the research of this particular UFO. If yes, you can do this:
alienDeployments:
- type: STR_SMALL_SCOUT
unlockedResearch: STR_SMALL_SCOUT
This should automatically give you research on the Small Scout if you win a ground battle with it. Note that you won't get the research if you abandon the mission.