1. How do I get enough Liberals/Socialists in my upper house to enact political and social reforms? Other than just choosing the "liberal" options for events.
Allow your POPs' CON to rise. That makes them "think" about their political aspirations, want political reforms, etc, thus turning them Liberal. Socialism usually follows that, once it is globally activated, and can be increased by increasing the level of Trade Union reform.
2. How do I promote craftsmen without using a NF?
Having high Administrative Efficiency allows for faster POP promotion/demotion all around, so that is the first step. Next, research technologies that reduce the RGO size and increase RGO productivity (Practical Steam Engine, etc). These will lower the price on RGO goods, making them less able to support large numbers of POPs and make more of them unemployed. Unemployed Laborers and Farmers demote to Craftsmen if you have jobs available in your Factories.
3. Why can I only "conquest" some uncivs and "Establish as Protectorate" others? As a civilised nation some uncivs I can only conquer and some uncivs I can conquer or Establish protectorate. Persia, even when it was down to one region I could only "conquer". But Ethiopia I could "Establish Protectorate", even if it was reasonably large from taking some land off Egypt. What gives?
It is based on the # of regions an Unciv has and whether or not you have researched Nationalism & Imperialism. Before that tech, you can only use "Protectorate" on one state uncivs. After, you can only use it on Uncivs with five or fewer states. Did you research this tech between the two wars?
4. What is the best way to raise the population of you main culture to increase the amount of NF's?
If there are any countries outside of yours with the same culture, conquer them (German and Italian minors). Researching techs that provide population growth helps, though it increases everyone's growth rate. Implementing Health Care is a huge helpl. Lastly, seek to minimize emigration through reform and satisfying POP needs. Emigration is a huge growth killer.
5. How do I get more promotions to Clerks other than using an NF?
1. Have high administrative efficiency from Bureaucrats. Increases Promotion/Demotion.
2. High literacy.
3. Meet your craftsmens' goods needs. POPs don't like to promote unless they are doing well financially.
6. What's the best army composition ratio. Infantry : Cav : Artillery : Tanks : Planes, etc?
It varies throughout the game and depends on what technologies/inventions you have. Here is what I usually field in my armies
Pre-Guards:
1-2 Cavalry
5-8 Infantry
4-6 Artillery
Guards, Pre-Tanks
0 Cavalry (I find they die really easily and I hate having to replace brigades)
6-8 Guards
4-6 Artillery
Tanks/Planes
2-3 Aeroplanes
2-3 Tanks
4-6 Artillery
8-10 Guards
My late game armies need to be redone, since I don't have much experience that late in the game (slow computer). I aim for a 2:3 ratio of Artillery to Infantry/Guards. Guards provide excellent Recon, which greatly reduces the need for Cavalry of any sort, unless you are looking for a fast moving territory occupying force. Then I use 3-4 brigades of Cavalry to snatch provinces from my enemy while I grind down his armies with my main armies.