I had the same thing happen to me. I have a 2006 rhino. It is basically stock. I don't have a CDI box, it only increases the rev limiter so you can get more top end speed but not anymore torque. I did place a Fuel gauge, volt meter, water temp and oil pressure. I like knowing the water temp especially. Back to the loss of power. I did build a custom snorkle on mine w/ 2" ID PVC with a secondary filter at the top. I didn't do anything to the stock air box, just placed a plummer rubber coupler to tie in the PVC to air box. I went down the road and it didn't seem to anything to the acceleration or top end speed. I went to the mountains a month later and it had horrible torque and was running hot. When the rhino is under alittle load or going up hills is when I noticed the torque was horrible. Of course I didn't change the jetting. I read alot of forums and they explained about running the engine after changing the jetting and reading the spark plug and/or waiting for a hard or soft stumble on acceleration, etc. I did everything from changing the slow jet, main jet and adding washers to needle jet. Basically I wanted low end torque. This is what I did.
I changed the slow jet to a 45, added 1 washer to the needle jet. When the rhino is under heavy load that is when you can tell if you have the right jet. I tied my rhino up to a tree and had it on my driveway. Each time I went up on the jet I tried to spin the tires on both 2 wheel drive and 4 wheel drive. I think I went up to a 175 main jet on mine. All 4 wheels spun on my driveway while tied up to a tree. If you go too small or too big on the jet it will lose power and of course won't spin the wheels. I didn't punch the gas, I just slowly gave it gas until the wheels started to spin. This should help.
To increase torgue you can add one washer between the sheave so the belt rides lower in the sheave to increase torque. Your top end speed will decrease about 4 mph.