1. What is the best way to avoid or survive the grenades on first 1-2 turns coming out of a ship? This is the main cause of reloads. It was depressing to have a first turn pass on the same old cult manor map , and have some kind of grenade kill your best troops. I was able to get better at surviving this by having good enough accuracy to kill most visible troops at first turn, but with leaving troop transports? What should be done? I did get a habit of throwing smoke but it sometimes is not enough
Do not go on cult etc. missions at daytime (but to monsters missions yes). Do not use crafts which have exterior lighting (e.g. dragonfly). Use smoke grenades before deploy. Skip the first turn completely if you're safe inside the craft (to avoid enemy reactions with full TU). You don't need to do all of these, but one or more of these will definitely help, depending on circumstances.
The night time deployment is usually the only thing I have needed or used against cults. Essentially you throw out flares and deal with the exposed enemies with grenades. But you'll have to be extra careful if once you deploy an enemy units sees you immediately, and in some cases you may need to abort then (due to the sniper/spotter described below).
You will need to learn the sniper/spotter mechanic. That is, certain enemy units are 'spotters'. If they see you or you hit them directly, all the 'snipers' can also shoot and throw grenades at you.
http://xcf.trigramreactor.net is your friend in browsing enemy unit descriptions.
You'll need to either deal with all the spotters in non-direct ways (e.g. throw grenades, not shoot them), all the snipers before you hit spotters directly, or have some kind of cover (certain crafts, buildings, etc.) which will prevent firing and grenades.
These have been my keys to SH IM campaigns. You almost never get grenaded if you strictly follow these principles.
2. How do you aquire the railguns for your troops? I was lucky in my playthrough to aquire some type of research for it early so I had railgun cannons for my interceptors, but had no way to give them to my troops, not having aquired an actual troop style gun. Is it perhaps in the under ground missions? Or do only certain aliens have it? I just like the idea of them and would like to know where to find them in the first place. I had lasers and sonic weapons and had yet to find one
There is no such weapon as 'railgun' in the game. I guess this is a translation issue and you refer to something else, but I have no idea what.
You don't need interceptors until 1999, though at certain point the syndicate retaliates against one of your bases. YMMV whether you want to shoot it down or let it pass.
Black-ops Sniper Rifle and Auto-Sniper are probably the best weapons in the early game, because like most other snipers, armor is only 75% effective and when you have maxed accuracy, they are very accurate and deadly. Before you get to them, you'll probably need to go through at least hunting rifles and bolt rifles. You'll obviously also need shotguns for close combat against lightly armored enemies. In the early or mid-game, that's essentially all the guns you absolutely must have.
3. Is tonfer better than the starting beat stick?
I guess you refer to 'tonfa'. For stunning enemies at close range, I suggest electric club, then briefly electric prod, and finally once you get it, stun rod. For further away, shotgun with blunt batons in the very early game (unarmored opponents), later MILKOR or grenade launcher with blunt ammo.
4. Is it a bad idea to shoot down every small UFO? I read comments year ago on youtube that it is like hitting a hornet nest and best to leave most of them alone if score can manage this.
There are two playstyles (at least in vanilla). In one, you avoid shooting down anything, because then the aliens will not start retaliation missions against your bases and you get the UFO intact. In the second, you shoot down everything (also the retaliating alien craft, but if they get big enough, you no longer can). I think by far the more common strategy is shooting down everything you can.
5. Is it really so bad to leave missions unattended if you don't need the people or the items in them anymore? As long as dont start going too low on score? youtube playthrough years ago, they had so many missions and so many UFOs that they ignored probably more than half of them, yet still won the game. I wonder if this is still viable? (They would sometimes land somewhere and immediently abandon for no negative score). I do know some missions start to really get annoying to do for the 20th time
You can check the despawn and abort penalties of each mission in xcf.trigramreactor.net.
In the first two-three years or so, I'd strongly recommend doing all the missions you can (and abort only those which you have no chance at). In the first 6-12 months or so, there are plenty of missions you have no chance at, so you may need to do 'go there, shoot for XP and abort' a dozen or more times in your campaign. You should already know which missions are doable with the resources and crafts you have. The game gets much easier if you get bigger score and better funding from the council based on good scores, so you'll definitely want to maximise your score, not just struggle along.
In the late game, when the money is no longer a faction, you can likely skip many missions if you don't want to bother.
6. If you shoot down a UFO and do not go there later, is this negative score? Is this worse than just leaving it alone for score? What is best practice for UFOS that you do not care too much about or perhaps that is too difficult at the moment
You get points for shooting down. AFAIK, there are no negative points for ignoring shot-down ufo. But obviously you don't get the points which you'd get from killing or capturing the aliens and all the loot. So, going after everything that you can handle is strongly advisable until the point when the money is no longer an issue.
