Whirring sound that increases with speed while in gear

Maybe a u-joint? When is the last time you greased them all? That's where I would start at least.
 
No but wouldn't that persist when I put the clutch in?
Yes. Sorry, I missed that part. I hear so many Jeeps running around here "whoop-whooping" with cupped tires, that was the first thing I thought of when I read it :), and I always think to check the most obvious things to start. Without really hearing it, I'm not sure where else to look, and I don't have much experience with the manuals.
 
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Whirring is such a broad term, I wouldn't know where to start. When I got engine electrical interference through my amp, a whirring noise came from my speakers. I have heard glazed brake pads make some strange noises as could a throw out or pilot shaft bearing. I would spend some free time crawling around all four corners and everything in between trying a process of elimination for the components that move. U-joints are a great place to start, the advice about the ring and pinion is sound as well. I had a bad ring and pinion and it gave off what I would describe as a howling noise. Side note: these Jeeps can be noisy buggers, but most sounds are symptoms of wear, lack of lubrication or influence of foreign substances. The good news, sooner or later, every noise gets identified, often though component failure. BTW, my NV3550 is in perfect health (for now) and it is a noisy box of growling rocks when compared to most transmissions. Don't be afraid to change your gear oil using Red Line MTL. Expensive, but it is definitely kind to the guts of your tranny. It quieted down my first tranny a lot. I found a replacement with very low miles so I swapped it, the engine and transfer at the same time. Deal was too good to pass up. Came from a RHD Japanese rig that was pampered on pavement and only saw about 25-30K miles.
 
When's the last time you checked your transmission fluid? It could be low or cruddy. Drain it out, then refill with a good quality gear lube. While this may cure your problem be sure to try and see what your clutch looks like too.
Every new (to me) vehicle I get I always replace all the fluids as soon as I can. Axles, trans, transfer, engine, coolant, brake, p.s. and grease fittings. That way I can normally spot any problems before they become terminal. Gets me familiar with all the suspension and steering components to see what is needed there too.