You keep coming back to it, but there is nothing you've said to indicate that you have a problem with the VCU.
Under inflated tyres are far worse than VCUs stiffening up. It will wear your transmission down to breaking point quite quickly. Lets hope it wasn't like it for to long and hasn't done to much damage. Your humming may or may not be related to it. If I was you, I'd start with the low cost options that are good for general maintenance or diagnostics...
1) Change the oil in your IRD. If the old oil is quite grey, suspect damage to the IRD and possible need for a reconditioned unit at some point. If its not grey, the unit should be healthy. 'Grey' indicates worn down bearings.
2) See if there's a lot of movement in the rear diff, eg push the front of it up and down. If there is movement, replace the mounting bushes. It seams most Freelanders over a certain age have needed these replaced, but my '99 hasn't so can't give specifics on replacement - but from viewing threads on here its usually the front one (of 3) that goes and is the easiest to replace.
3) Take Bukko's advice and remove the props. Its a 30 minute job, just undo the (star) bolts joining them to the IRD & rear diff plus the bolts supporting the VCU and take it away - be careful though its heavy and you don't want it dropping on you or damaging it by over extending the UJs. With the props removed you can still drive the car, plenty are driven permanently like this, and can't really do any more damage to the transmission unless something is on the brink of letting go. With the props off you can check the condition of the VCU bearings which are another item that commonly need replacing and cause noises.
With the props off you can reassess the noises. Likelyhood is they'll stop. Jamesmartin's advice on rear diff pinion bearings sounds good so with low-cost options eliminated will be worth doing/considering. If you don't, at least change the oil. If the sounds persist, I'm sure I've read similar threads on here to yours that has just turned out to be the exhaust rubbing against something (or similar). So check to make sure everything looks OK and the exhaust hasn't shifted or dropped off a mount or something.
I'd also say noises can 'travel' through the car, you think its coming from somewhere, but its actually coming from somewhere else. There's threads on here at the moment where people are getting mechanics stethoscopes to try and confirm where noises are coming from, not sure if this could help to listen out of overrun - but you get my point. If you take your hippo to a garage they may be able to put it on a hoist and listen to the bearings in your diff to confirm they are shot, rather like the MOT bod feels for shot wheel bearings.