@Will- My opinion on your engine noise from my experience, it may help.
There are very few things in UCE which can make noise as per your bike at present condition. I'll try to explain so you can go step by step to find it yourself the source of the noise.
1. Lets start with Hydraulic lifters- If there is any problem with the lifters, usually you will loose compression or you will have starting/running problem. In your case you have none. To simply check if you have any problem with them, take off the rocker cover and try to rotate the push rods. If you find any play then you have a lead.
2. You can also loosen up the rockers and remove the push rods to inspect their ends. Highly unlikely that you will find anything wrong with the push rods or hydraulic lifters.
Anyways I know your noise is in the bottom half so I wont clarify above two more then required.
3. Big end/ con rod bearing- If that had gone bad then you will hear piston slap of abnormal proportions and you will easily identify it as it increases with load and even on idle, you will find it hard to cover your face at traffic lights. You will get undivided attention. I rode more then 1K miles with a blown big end and it could have done more so don't worry if you think you might get stranded in middle of the road. But i'll still say it's over built and one in a 100 chance of failure rate.
4. OIl pump- When you remove the rocker cover, crank the engine with plug leads off for more then 5 seconds and if you see the oil spewing out of the rocker dowel then eliminate that too.
My suspicion is on the crank RHS NRB or the cams.
5. Cams- Usually on a UCE if the sleeve of the cam gets worn out and the cam develops more then required lash then it produces a howling knock/grinding kind of noise. I don't think you have that either. But you would know more as my ability to hear your source of noise is as good as your recording equipment.
6. If cams develops marks on it's lobe from the hydraulic lifter roller then again you would know after having a look at it.
You do not need any special tools to remove the cam on a UCE. All you need to do is remove the rotor on the crank shaft and the plate with three 5 size allen key bolts to access the cams for removal. Although you can make your life easy if you loosen up the rockers so you won't need to panic when lifters will jam on the cam shaft after you remove the cams.
If I can remove the cams without any proper tools. I am sure you can do better.
7. Before you are done with probing the cams for any wear/ issues, just do one simple test to eliminate the crank shaft NRB as this is one thing which will require a strip down of the engine.
After you have removed the cams, hold the RHS crank shaft tip and move it up/down with a bit of pressure. Feel for any play, I mean literally any jitter and if you sense any play in the shaft then you have found your source of noise. If you are unfortunate enough to find the play then all you can do is strip down and replace the NRB and it will go again in near future unless you can source a German NRB bearing for the replacement which RE is trying so hard to source but the Germans(INA make) are not interested to supply them with only few k's per month. I tried sourcing from FAG but they wont sell me just one piece. Don't even go near a SKF thats what we have now.
8. If the crank shaft has no play then you can still try one more thing. Remove the head/barrel, hold the con rod and push/pull up/down to feel any play in the big end. There is a wee bit of play of con rod sideways and thats totally company specs so dont bother with that but if you feel any up/down play then you would need a new crank. It wont take more then 1 hr to remove the head/barrel and replace it back so you can DIY.
So to sum up there are only three main areas you should look for the noise issue.
1. Start with cams
2. Crank shaft NRB
3. BIg end
For all these you dont need to strip you engine just for the diagnostic. Trust me with the simple methods I have explained to find the culprit, specially with the crank shaft NRB. When I had the same issue twice, I had challenged the UCE R&D head along with the two RE engineers to trace the issue within 24hrs and after spending the whole day playing with the engine they were silent. Only to hear from me that I know what was the issue and I will only tell them after they replace the crank/barrel/piston. Eventually I told them and after one whole year they want to replace the NRB on production bikes.
If you need any more clarification then let me know.