It's probably the Neck Bearings. The 08's had a Bulletin out on the Fairing bracket's. Mine were replaced under warranty. Didn't know it was out , my Dealer Service manager informed me.

 

For OP...can you get the bike elevated (jack) & start looking/wiggling things around? Could be a number of things (from neck/wheel bearing to loose bolts/fairing bracket). Best to get the bike elevated & free so you can start tracing down the cause...

 

I have the clunk on my '07. but I believe mine is "topping out", not bottoming out. I definately need a fork oil change for sure but haven't done it yet. I have already done the steering head bearing tightness check and it's good, tank is good too and so are fairing brackets.

This brings me to a quesiton: what color are the forks on a stock '07 Ultra? Mine are black.

 

I have owned 3 harleys and they all did the chunt, klunk thing when encountering
a chuck hole. Worried the ship out of me on the first one, I was thiking neck
bearing. But NO!!! So I just let her chunk and klunk, and I wont worry and am
mosely happy ..........Be happy dont worrry................

 

When my Profile springs were installed they installed the washers wrong and subsequently caused a clank. They fixed under warranty with new hardware and the clank went away

 

I have checked the gas tank, front fender bolts, fairing brackets, I just had the front wheel bearings replaced ( warranty) The front forks are all stock, including the fluid, Im thinking fluid change, would it make that much difference?

 

Another possibility; stock progressive rate springs are soft in about their first inch of travel, on a sharp bump the pressure spikes rapidly in the lower fork, the valve can not relieve the pressure fast enough, the excess pressure pushes the entire valve body upward and it overwhelms the resistance of the weaker rate section of the spring at first, then when the pressure subsides the spring slams it back down. I have experienced this with both the OEM valves and the Ricor Intiminators and with stock and aftermarket springs, it only happens on very sharp bumps. Simply put high velocity compliance is insufficient; the valve momentarily floating off its seat makes up the pressure relief difference. There are a lot of things that can cause a clunk in the front end, if everything else checks out, then the valve floating may be what you are experiencing.