The issue I'm having is at high speeds. Around 40 mph, I can hear what sounds like a typical noise a tire would make (like on a truck) but then I start getting a clunking sound almost like something hitting the underneath of the car.
As you increase speed it gets louder but no vibration in the wheel and there is no bouncing in the struts.
So I have ordered new axles. Seems likely it could be the inner cv joint. Anyone else encounter this problem before. Any input would be appreciated.

Oh the tires have about 10k on them, just rotated and balanced. The back tires did have some cupping on the outside of the tires.

 

I don't have a fix for you and I have never encountered this.

How many miles on the CV joints? Are they original to the car or is this a different set? How many miles do you figure are on the CV's? How many miles on the car if not the original joints?

 

They are original to the car and have 143k on them. Replacing both to see if that is the problem.

 

Two things about your post got my attention.
(1) Clunking noise but no vibration. If the cv axles were bad enough to clunk,I would think they would vibrate.
(2) Cupping of the rear tires.If they cupped,you had a vibration. You may not have noticed it. I would think this is rear shocks. Cv axles aren't going to cause this problem in the rear. AND,cupped tires are probably going to make some extra road noise(like mud tires).
HHR's are known for their suspension parts to wear out pre-maturely. I am guessing with your mileage that you most likely have more than one suspension part that is worn out.

 

I'm thinking that inner CV failure is an unlikely culprit here, as firemangeorge has stated, check the tires and suspension components carefully.

Unless an inner joint has a damaged boot and has been run huge mileages, they just almost never fail.

 

My most recent ox is the control arm bushings. They seem to be the weak point in the suspension, and are too difficult to see to be routinely checked.

My old ox was the hub bearings, if you are already committed to replacing the axles, it's no more work to replace the hubs, since you have to remove them to get the axles out.

 

I figured at 60 a pop for axles. I would replace them.

Axles replaced and I must say it was very easy and looks like everything else will be fairly easy also. The drivers side hub would not spin freely and I ordered one from autozone. Well, told autozone I didn't need it and promptly got my 188 dollars back so I can order 2 for 220 from partstrain.com.
Anyway, after changing the axles, the clunking is gone but the roar is still there. Gonna order the KYB struts and shocks as this is the way to go from what I've been reading. Also gonna change bushings for sway bar and outer tie rods.
What is the best way to go about replacing the lower control arm? Change bushings or whole arm and if so, what arm is the best to go with? After that, stabilizer bars are all that's left I believe?
I do feel that the hub is the main culprit here and with everything being so worn just made it hard to diagnose.

 

You didn't mention a roar, that's for sure hubs! I wouldn't bother with tie rod ends, the rarely go bad & then would have to get an alignment done. Lower control arms are a breeze to just replace plus you get new ball joint and new front bushing, however new bushings are real cheap $13 IF you can find the right tool to press them in/out. I got the Dorman 521-025/026 from RockAuto around $85 each, when you add everything you get plus labor time, that's a pretty good deal. Be careful when ordering, some of control arms out there will fit, but are Cobalt parts i.e. they are powder coated steel not cast Aluminum, I don't know an argument either way or another just that stock is cast on the HHR. Stabilizer (sway bar) links, shop around I got a pair for $32 and bushings are cheap and easy and make noises if worn out.

 

The roar became more noticeable after the clunking stopped. Not familiar with these type of bearings although they are easy to change. I grabbed the tire everywhere and there was no play so I assumed they were good.
I know, never assume anything.

 

Unfortunately the acceptable play on these bearings is so tiny you need the good stuff to diagnose before they become dead on the highway.