Oh. Well, I've completely borked my playthrough xD.
Oh! I remembered more questions that I had...
With Smoke Grenades, where do I throw them, in relation to enemy forces?
Generally, throw them where your troops are, or between your troops and the enemy (closer to you). Avoid throwing at the enemy. The main reason is that smoke grenades essentially add squares to vision range. If it covers your soldiers, then you have really good control over who you can and can't see (by moving into or out of the smoke), and each square of smoke you move through means an enemy has to move through several squares. The general strategy is to deploy the smoke, walk out and spot an enemy, shoot them directly (if you can risk the reaction fire), or walk back and shoot them blindly (or with another soldier).
However, many animals and aliens have some sort of thermal vision and/or PSI vision. Those can partially or completely negate any benefits of smoke. If you have their combat stats, you can check for those abilities in the Info screen. Note that your own dogs also have thermal vision, so use this to your advantage!
Another important note is that if you hit any enemies on your turn (or their turn) with a shot (or direct hit from a grenade launcher), you're automatically "known" to the enemy until the end of their turn. Many enemies in this game can shoot you if they "know" about you, so smoke may be way less effective if you've hit anyone on your turn. Red Dawn has many enemies like this, so if you want to use smoke grenades, make sure you can either find hard cover or throw grenades instead.
Are handcuffs worth using?
Occasionally. Some enemies tend to recover stun damage much faster than normal. Some are just that important and I don't want to have to deal with them.
Did I build a 2nd base too early?
Rather than a time, I look at money. I usually try to build a second base when I have about 2 million dollars. That's about how much to get a new base up and running (Hanger + Stores + Quarters + Gym + construction cost). I also try to start saving for the Intelligence Center so that I can immediately increase my research capacity.
I almost obsessively kneel....is that bad? Does kneeling provide any benefit other than accuracy?
It makes you slightly harder to hit too. In some cases (kneeling behind your car, for example), it can block line-of-sight.
As I've gotten better at the game, I definitely find myself kneeling a bit less. It's usually better to keep your mobility and move out of sight behind a solid wall, or into dense smoke. I'll kneel if there's not much else I can do, or if I need to make an important shot and have the TUs to spare. However, keep in mind that kneeling can mess up line-of-sight, so I try not to do that unless I'm sure that it won't mess things up.
Well, wrt the promotion II timing, I guess a question is "What's a typical/par-for-the-course" timeframe? I'm trying to gauge just how much I botched my playthrough 
I usually try to get that around September or October of 1997 if I can. However, there's a luck component that's out of your control -- you need to get a researchable Cool Alien Gadget (usually a Psi Clone) and the 2nd tier of cultists from all 4 cults. One recent game, I did not get a single EXALT Safehouse until December, even though I had researched EXALT either in Jan or Feb. In a different game, it took me a very long time to find a Psi Clone. The main advantage of having Promotion 2 early is that you can get access to Armored Vests, which makes a huge difference in casualty rates.
It's not too big of a deal if you get to it early 1998, because before then, it's hard to have enough money to build a lab and hire 25 scientists. You won't be at risk of falling behind in research as long as you make sure to save up money to get the lab as soon as its unlocked.
Sorry for all my chump/newb questions...
No problem. I like answering these, because often the discussion leads to me getting better too.
Start of game, I would say the most important research are: Logistics (Van), Kevlar Vests (basic protection for cult missions), and Promotion 1 (smoke grenades). After that, try to get Dogs (helps a ton with undercover missions which are money makers), followed by the Helicopter to get 6 Soldiers out on missions. Better weapons can usually wait a bit, since you'll likely loot plenty of rifles that you can immediately use. However, the Hunting Rifle is pretty darn good.
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