The game manual is sadly out of date. I don't have a link to a game guide to give you, but I hope someone else will post one since I have seen similar requests in the past.

To address your specific questions, the production wheel was removed a while back (after many complaints that it forced micromanagement) and the manual never updated.  One way you can still shift civilization focus from social manufacturing to research to ship production etc is to use Leader type citizens, and move them from one focus area to another on the first page of the civilization window.  When you trade a new leader it automatically gets assigned to the top focus area on that page.  Click on the leader to move it to the bottom (unassigned) then click on an empty slot on the focus area you want it assigned to.  More focus areas become available as you research their enabling techs.

I don't see any downside to Open Borders treaties.  Having one will raise the disposition of most opponents, while not having one will make them view you unfavorably if any of your ships are in their zone of control, but will not stop them from sailing into your zone of control.

And yes, the trade offers the AIs make to you are usually terrible trades.  I usually just offer them open borders for cash, and turn down all their offers.  There are diplomatic techs and ideology perks that can improve the balance of the trade offers.

I have to agree with @Franton on his trade recommendations.  And his recommendation to turn off trade brokering (which I also do) reminded me of another setting that often trips up new players.  Each planet has a setting on its Govern window to "Auto-Upgrade Improvements".  While this does cut down on micro management, I always turn it off (on each and every planet) because it can drain resources you'd like to prioritize elsewhere. For example, the higher tiers of factories require durantium to upgrade, and I often would rather use that durantium to upgrade a starbase or build something else rather than have the game automatically use it to get me a 2.5% improvement to a factory.

You can take over planets and asteroid mines with influence, but not starbases or mined resources.  So you can't take over his mining starbase or his durantium resource.

Generally I use influence starbases to try to flip an opponent's planet or defend my own from flipping.  As far as I know the best placement is so that the planet involved is within the starbase's range of effect.  I suspect that further away works also but not as effectively.

Note that building a consulate on your planet and/or other influence improvements is an alternative to using an influence starbase.  Expanding your zone of influence is also important for tourism income, although I think you said that you only have Crusade and I can't remember whether tourism is as big a deal in Crusade as it was in the Intrigue and Retribution DLCs (before the recent partial nerf).

One basic tip- learn to use the starship editor early. Many default designs can be easily optimized by simply removing unnecessary parts- thus making them easier to build.

For any combat, even 1 defensive device of the matching type (i.e shields for beam attacks) on a ship cam make a big difference in survival rates.

When building improvements, use special tiles and adjacency bonuses- those can stack and make a huge difference in the overall planetary output

Lastly, use cargo hulls to make wide area radar picket ships to keep yourself from being surprised. Even in the beginning, a cargo ship with a few sensors and engines can help you on the exploration- to find useful planets and resources before the other folks find them. The default scouts are too small/slow for effective exploration...

Thanks for all the info and tips.  It's helping a lot.  I have also started watching the GC3 Crusade Let's Play you tube series.  That seems to be pretty good so far.

So I flipped a planet recently (it took a while to flip it even after my influence completely enveloped the planet), but it doesn't seem like I gained complete control of it.  If I try and move a ship onto it, I get a message about starting a war and the shipyard built by it is still controlled by my opponent.  I can control the tile improvements and I believe I get all the planetary resources; wealth, construction, etc.

I also have recently had war declared against me.  Looking for any tips/help on what to do/think about as far as defending myself, and also strategies about invading my opponents planets.  Not even sure where to start as far as offensive and defensive operations are concerned (I haven't gotten that far in the Let's Play series hopefully that will help). 

It happens a lot where civs from across the galaxy will declare war on you, even if they cannot reach you.  This may not even be an issue, if you grow some fleets and attack one of their scout ships, they may ask for peace.  Or, they might start building starbases to reach you.  Don't be too annoyed by the graphs, fleet strength is often no true measure for how well they will hold up to an actual war.  I have found, the best way to up your fleet graph is to go for Kinetic weapons, which is the smallest, cheapest, no-resource weapon in the earliest parts of the game.  Beef up some ships with nothing but kinetics, and if it is early enough in the game, it'll skyrocket your fleet graph.  That may be enough for enemy civs to ask for peace.

I agree with the idea of protecting all planets with at least one basic attack ship, no matter how weak it is, just to prevent easy planetary takeover.

Wow. I too wondered what that "You know what you did" meant. No I definitiely did not know what I did! I had no idea at all! This should either be stated clearly in the tool tips, or 'open borders' should be renamed appropriately. How are you supposed to know what it means otherwise?

I really want to like this game, but I just keep stumbling over things that don't work as advertised or expected, because SD failed to provide adequate and up to date information in game.

I recommend getting off the classic version. Play the latest version. I think it is 3.7, even opting into betas as long as they work. That is best for balance. Crusades is better for tourism. I recently played crusades only in multiplayer. If you don't have mercenaries installed I would recommend rush buying paxton emporium. As far as mercenaries I use them for exploration the most. I recommend the prospector, super, or sabel. Remember the prospector is a survey not a war ship. 

I would build the space elevator as soon as I colonise a planet. Right after I build my first shipyard. I use constructors to build the other shipyards, unless I start with a constructors. If that is the case use it to build a shipyard. No more than 7 spaces away from at least 1 planet. I try to get it connected that way to as many planets as I can. You can move it later to do this. I don't move it out of star systems it's to slow. So you can load colony ships. As far as distance decay I use an arbitrary number of 50 percent. Make sure all your planets are sponsering shipyards.

A good way to get raw production is build asteroid mines. 

I would explore with custom built cargo hull survey ships. 

You can decommission the transport and the legions return to your pool.  I only build and keep transports when I need them.

I signed a peace treaty with the Drengin, so I won't be attempting to invade for a while.

I'm now trying to understand colony improvements.  Specifically affects and adjacency bonus.  On the wiki there are 3 columns for each improvement; affects, level affects, and neighbor bonuses.  Not sure what the difference is between affects and level affects?  Is the level affects multiplied per level of the improvement?

For example a Basic Factory is listed as Colony Manufacturing +15% for affects, Colony Manufacturing +5% for level affects, and Colony Manufacturing +1 for neighbor bonus.  While a Xeno Factory is listed as Colony Manufacturing +25% for affects, Colony Manufacturing +5% for level affects, and Colony Manufacturing +1 for neighbor bonus.  I'm assuming that a Basic Factory is a Level 1 while a Xeno Factory is Level 2 (I don't see the levels listed in the wiki)?  So does a Basic Factory get a 20% [15%+(1*5%)] increase to manufacturing while a Xeno Factory would get 35% [25%+(2*5%)]?  Then if you put 2 factories next to each other would you also get a +2 bonus to manufacturing (each getting a +1 from each other for adjacency bonus)?  And if you put 3 next to each other in a triangle fashion, would you get a total of +6 bonus (+2 for each one)? 

I have not found this kind of detail explained well anywhere.

Thanks Horemvore, but your reply still has me confused.

The numbers you posted are different than what I posted from the wiki.  Did I get the info incorrectly from the wiki, or is the wiki incorrect/outdated?

I also did not follow your explanation.  Could you or someone break it down further?  I take it you came up with 7% for factory next to factory by adding Effect plus Level Effect (2.5% + 1% = 3.5%) for each factory and then adding each Factory (3.5% + 3.5% = 7%)?

I guess I'm still not sure exactly what the difference between Effect, Level Affect, and Adjacency are?  Does Level Affect only apply if adjacent?  Where does the +1  for adjacency apply  in the calculation?  What if the Adjacency was a +2?

OK, thanks that explanation helps.

Effect - what bonus the building gives on its own, with no adjacency bonus

Adjacency - the number of levels given to buildings next to it, of the appropriate type

Level - the number of levels given to that building, by adjacencies (or special tiles)