I've been playing XCOM Files recently after not having played any kind of XCOM game in many years. I abandoned my first attempt because of probably similar feelings that I was doing really badly on research, but I feel my current (second) playthrough is going pretty well. What I've done differently is to devote lots of resources to advancing research, but at the same time not really be too concerned about the results.
This mod is a lot different from XCOM (as I remember it) in the research aspect. There are an almost overwhelming number of research topics, and even with dozens of scientists it will be years of in-game time before you can catch up. But I think the important thing about research is just the cumulative advancement. Most of the research topics don't directly help your cause much, but added together they allow you to make modest improvements over time. In other words, it's not like XCOM, where you're researching to quickly get some flying armor, a supergun, and an awesome attack ship. It's a long process in this mod, so be patient. And the mod allows you to be patient, since no particular research is critical.
What I've found so far is that the key to advancing research doesn't have anything to do with research. Do as many missions as you can, month after month, and keep bringing in the money. This allows you to build more bases, with more labs and more scientists. As you do that, research progress develops naturally.
Get your research started by looking into medical-related topics. This allows you to get the Bio-Lab, and put more scientists to work.
I'd also recommend not focusing too much on researching every gang or cult related topic right away. You'll just be overwhelmed, without making much overall progress. Instead, focus on taking down one organization at a time. This gives you a better feeling for each story arc, like your agents are conducting a real investigation in each case, gathering evidence and making arrests that matter.
Overall, I suggest an early game research strategy focused on getting better labs and getting faster/larger vehicles. The latter allows you to respond to more alerts, and get more money which you can use to hire more scientists. You're not going to get any weapons or armor breakthroughs for a long time, but the good news is you don't really need them for a long time, either. A magnum revolver, a stun rod, and a kevlar vest is all your agents will need for the first few years of in-game time.