I am guessing that because others have mentioned something similar, that the answer might be no, there isnt really a beginners guide.

There are several posts aimed at beginners ,and there are also links to official tutorials, recently there have been several  posts by one of the administrators, which are aimed at new players, and as a reminder to more seasoned ones.

There are also the links on the start up page of the web browser version, I do not know where these links might be on other versions.

There are also guides on the web, including youtube, but these seem to be for older versions of the game.

A good way is learning from a good clan chief, the drawback to this is, that you might follow advice not to your game strategy ,or learn the same mistakes the chief made, even good advice might be not as relevant as the game has changed considerably.

As to missing buildings,I am not sure what you mean.You can not upgrade buildings that are not there, you have to build them first, except for the ones the game gives you at the start.

The game gives you various conflicts of interest as to what to do and when.

Being in a clan and concentraing on invader skills is a good way to go, however lots of players just want to build troops, attack other players and then become unstuck.

Help is available for those that ask and want to learn to play better,though it has flaws, its basically a good game , but the best advice is quit now.

If you are planning to stick around, its worth considering buying the offers for equipment of the north, and if it is still offered, the novice pack.

Its worth your while logging on for 30 days  to take advantage of the "free" stuff.  Bank, calendar, and quests and tasks.

The missing buildings I am referring to show in the stats in my profile.  I know they are there, but I can't see them when I log in, even after I zoom out.  Sometimes, I can't see my watch tower, for instance.  Other times, it is farms or mines.  

The way you describe this, its not consistent, in any case as far as I can tell, it shouldn't be happening at all. 

Do you know how to post screen shots?

 It would help the administrators deal with the problem if you could do this, and possibly more information about what happens and when.

You could wait for them to reply here , or contact Ivar Marksman  directly.