I think that for this first year you should just work on optimizing what you have. A little basic maintenance and a few simple bolt-on parts will help you achieve most of your goals at a very modest cost. An alternator upgrade is very common these days and should provide all the electrical power you will need. The early battery death you experienced might have been because of a bad voltage regulator. I'm not sure what's in there now, but the original one probably relied on lots of resistance coils and contact points to operate. There are modern solid state designs that might work better in a harsh environment.
As for your cooling issues, yes, start with a flush and thermostat. I'm not sure if there is room for an engine driven fan but if there is, the six-bladed 6 cyl AC fan blows (sucks?) better than the standard four-bladed fan. A bigger radiator might be possible as well. I don't know how much room there is there. I had to smile when you mentioned running the heaters to help cool the engine. I used to live in CO, and there were many times driving my '57 MGA that I had to run the heater full blast on a hot summer day when cresting a pass...
That engine would have usually had an automatic choke when in a car. Does the manual choke on your carburetor work? You'll need a working choke for cold starts. A coolant heater will warm the entire engine block and head, and some of that heat should get to the carb as well. I had an MGB GT I drove as a MN winter car one year, and put the biggest coolant heater I could fit in it. Despite sitting outside, it always started right up and the heater was even a little warm right away!
Engine modifications are possible, but you might want to assess what you have for a while first. A two barrel carburetor can be custom fitted either of two ways. You can leave the head on and mount the carb with an adaptor to fit the original small one barrel carb opening on the manifold. Much easier to do, but with minor gains. If you remove the head, the intake can be machined to enlarge the opening and put a proper two barrel mount on it. More cost and trouble, but with bigger gains. Either way you have to do some custom work with the linkages and lines connected to the carb. With the head off you could also do some milling to reduce the size of the combustion chambers to increase the compression ratio and increase the power a little. High RPM power is probably not what you want here, so headers with a dual exhaust, fancy cams and heavy valve springs and all that expensive machining and porting would be a waste. Or would it help the engine out at high altitude but low RPM enough to be worth it? The brainiacs on here can argue that point.
Forced induction in your Snowcat will be an enormous can of worms. If it could even be designed to fit in the doghouse, it will be very expensive as just about everything will have to be custom made. And then there's all the extra heat to be dealt with in an already overheated engine. This would not be an easy bolt-on process. I think it would be easier to just put in a different engine. Maybe a 250 would fit. If you can keep your upgrade expenses to a minimum with this current engine, switching to a bigger one if you decide that's needed down the road won't mean so much money tossed out with the old, and leave more for the in with the new. My two cents anyway.
