Low civilization settings are set but often entire landmass is filled up with cities.
Civilization settings are just for the number of possible civilizations there can be, not how many cities they can each have. Site limit controlls how many cities each civilization can have. It's an advanced setting. You can reduce this with standard generation by using smaller maps. I wouldn't worry about this too much for your first game though.
Most recently last few times I end up in some area with no mountain just gray ground snow no river,
That wasn't what I saw on the map.
Mountains are a bit of a misnomer on the map screen. Mountains only indicate high, rocky terrain, but not necesarrily peaks. High plateus will show up exactly the same as mountains. For actual montainous terrain you have to look at the cliffs indicator. To do this, on the embark site selection screen press tab 4 times. The local area will change to a bunch of numbers. This indicates how tortuous the terrain is. High numbers means more elevation variation.
Also, it is likely that your river is frozen and buried under the snow. You can search for it by going down one level (shift + .)
If you can post a picture of your embark site selection screen, I might be able to provide additional insight.
I can't zoom or move out any way to see if the lake has been hidden.
There really isn't any zooming per se in dwarf fortress. Your embark is bounded by your initial selection. If it's small enough and your screen resolution is large enough, it's possible your entire embark is on the screen. If I recall, the default embark size used by the newbie pack is 2x2.
Otherwise arrow keys and the side carrot keys should allow you to move around your embark.
Then I try to set up trying to move stuff off the cart with shortcut keys, which is often right in front of me.
Can you be smidge more specific here? How are you trying to have them moved?
I can't control plot size, I end up with weird shape ones
Are you talking about farm plots here, or stockpiles?
and when I try to set permissions for specific object or pasture areas for animals about here something just doesn't happen that I got no clue why this happen.
I am not sure what you're trying to say here.
Pastures work like this: Press i, move the cursor to where you want a corner, press enter to select your first corner, move the cursor to where you want the diagonal corner to be, hit enter again, then press 'n' to designate it as a pasture, then press N (shift + n) to bring up the animal selection menu to assign animals to the pasture. Once the animals are assigned to the pasture, the dwarves will move those animals to the pasture when they have a free moment to do so.
I try to dig a room last time I just kept hitting rock or worse yet I clear out entire space but all the rocks, clay are missing or I can't pick them up and put them in pile somewhere
Not everything leave a rock behind, and clay/dirt is never left behind. For your first fort, it's probably just better to ignore rock hauling and let your masons pick the rocks up off the ground whenever they are needed.
If you insist on stockpiling rock, you need to first designate a rock stockpile. Press 'p' to bring up the stockpile menu, 'r' to select rocks, position your cursor where you want the first corner of the stockpile to be, press 'enter', move the cursor to the diagonal corner of where you want the stockpile to be, press enter again.
Chop a bunch of trees maybe they will be cut, maybe not but either way I can't pick up the logs or get the dwarves to do it.
Again, this requires a wood stockpile, but is not necesarry. Your dwarves will happily pick up logs for any work they need to do with them. Best skip worrying about stockpiling the logs until later.
Set up a workshop with whatever I brought with me, takes my goods but doesn't seem to build or if I get farm or fishing plot open something else goes wrong.
Some workshops require architect (building designer) labor enabled. Make sure you have at least one dwarf with this labor enabled. Further, most workshops require the labor associated with that shop to be built. Make sure you have fish cleaning enabled on at least one dwarf before trying to build a fishing workshop.
Fishing workshop poofs like its not there even when I set the area as fishing area and water source.
There are two different things needed for fishing, and it sounds like you're confusing the two of them. The first is a fishing activity zone. This is the area you set up with the menu that opens with the 'i' key. That's not the shop, though. You have to build the shop using the build menu under 'b' and then the workshop menu 'w' within that menu. Fishing workship is then the 'h' key.
And there is more, like my picks are enabled in one version of the game and the other version of game it doesn't seem like it is.
I'm not sure what you're trying to say here. Do you mean sometimes your embark doesn't have any picks or that sometimes mining isn't enabled on your dwarves by default?
And if I select or unselect job task in Dwarf Therapist I run into problems too there.
Its like setting the task or something only partially happens that I don't entirely know how to explain,
Make sure to commit your changes when using dwarf therapist. It does not track your changes in real time. Even us old salts still forget to commit stuff and wonder why nothing is getting done.