Note. These answers are by no means definitive, and are all gleaned from my limited understanding of the situation.
1. About story vs temporary variables.
Generally, the issue you encounter with variables is related to the state history. Without going too far into the weeds, basically, using variables unwisely can cause slowdown as the game goes on in longer games. It is unlikely that the amount of information you're tracking could ever lead to noticeable slowdown, the problem lies in the fact that a copy of the entire state (including variables, passage names, etc) is passed to each new moment in the history. This has the effect of multiplying the number of variables being tracked.
So, in short, it's a best practice to use temporary variables when possible. Liberal and unnecessary use of story variables is always going to bog down your story on some level, but it's important to point out that this takes a lot.
2. About passage length vs number.
As far as I can tell, not really. The amount of passages may effect initial load times and some early transitions. I wouldn't worry about this. It could cut down on moments as mentioned above, which would indirectly help with any variable issues, but it's better to probably attack that problem from the variable side.
3. About links.
Generally, the standard double-square-bracket link. Using the (click:) macro forces the page to be reparsed, from my understanding. It is, quite literally, the slowest and most expensive possible way to create a link of all the available options. I wouldn't use it as a general replacement for normal links, which is what you seem to be doing.
4. About Harlowe 2.
Generally, using the most recent major version of anything is best. There are quite likely a number of optimizations and improvements that have and will come to 2.x that you'll never see. I would be surprised if 1.x received anything but major bug fixes and security fixes. Any new and exciting ways to improve performance will probably not make it to version 1. If possible, you should migrate over.