Check as many of the shipping runs as you can see. If they're civilian or government, they'll be a net infamy loss, so don't bug them unless they have something else you need. Actually attack a few of factions shipments each month, but after a few good missions it shouldn't be as important. Always try to at least make it to start a mission with a landed vessel, even if you know you can't fight it. If you land, start the mission, and abort right on the first turn, even before exiting your vessel, you at least abort the mission and prevent the faction from scoring points, which means less of reduction of your infamy at the end of the month.
Interrogations are generally questioning any prisoner, though later you can interrogate Broken members of certain class/factions. (Guild Engineer, Academy Medic, such as that.) Pimpcraft will allow you to turn certain female prisoners in COURTESANs (hookers) who generate income every month. $20k a month, if I recall correctly.
Generally, research every prisoner until you can't research them again. My preference is to pimp anyone I can, after that enslave. Only if they have something I can really use do I bother to rob them, otherwise I ransom them.
By year two you should already be able to distill Chateau de la Mort, it's very easy to get, with only one or two subjects really only good for Chateau de la Mort. It uses apples, but sells for a hell of a lot more than X-Grog, and you can still use X-Grog as a backup every time you run out of apples. Won't do much for infamy, but it does help with funding, which can help with equipment, which in turns helps with fights.
There also a few special researches to round certain branches of research, such as for each region of the world, or each type of activity. When you get all the researches completed in a category, you'll get something like World Lore: North America (for all the regions on the North American continent) or Activities: Political (for faction missions affecting government influence and such). Each of those is worth 1000 points.