I don't like the sound of my system. Help please.

For starters your ARC gear should be left on all the time for best sound. It can sound hard and thin until fully warmed up which can take up to 3 days for ARC solid state and hybrid preamps.

I have found ARC and Vandersteen to be a good match. However, my experience is not with the latest Vandersteens.

You should be able to warm up the sound by adjusting the REL.

Call John at the Audio Connection.

Also make sure speakers are hooked up properly in phase, ie red/+ to red/+, black/- to black/-, etc.

Something out of phase somewhere might account for what you describe. Speaker connections are most likely and easy to check and fix.

Also can we assume the Vandersteens and source electronics are all in good working order? IS there any noticeable distortion or more just the tonality is not meeting expectations?

Hopefully they are but only you could determine that for certain. The easy way if possible is to swap out one piece at a time and see if that makes a difference. I always like to keep a spare amp and pre-amp and an extra pair of decent speakers around to use for such things. A relatively inexpensive integrated amp with pre-out and power in connections, like a NAD or such, works well for this. You might even like the resulting sound better even if everything is working fine. That would be more of a judgement call at that point. If you buy something used and do not overpay, you can always resell and change as needed without a big financial hit until things work out.

I would not be quick to pair ARC and Naim; I can understand why you would have issues. The nature of these two house sounds would not be complementary, imo.

Further, if you are using stock cabling I would assert the weakenesses of each would contribute to quite a tough sound. Using a Vandy 2CE Sig one would not typically expect a thin and strained result, but that certainly could happen with those components and lesser wiring.

My assessment is that if you wish to move quite a distance away from the current sound you will likely need to change both the ARC and the Naim. Individually in properly established systems they can perform fine, but it sounds like you do not care for the result at all, so a sea change is in order. I do not believe that futzing with lesser fixes, i.e. burn in, even cable changes will ameliorate the larger issue. Treatment of the space is also not the issue; you cannot alter a fundamentally poor combination to your ears holistically by room treatment - the character of the system will be only partially ameliorated.

Now, if you do room treatment, cable change, adjust the sub, etc. you may - I say, may - get a nice enough change. However, I feel this is lowered expectations for you. You should use this frustration to seek a sea change in sound, not putz around with getting it "good enough." Seek a FAR higher, more pleasing result, one which will leave you shaking your head at how wonderful it is. Such changes can happen and do all the time. But it will take a changeout of components. If you want a smoother, less fatiguing result, keep the CJ and Vandies and rebuild.

You're doing well to have a forgiving speaker like the Vandy... or else it would be worse! :)

Suggestions?

Down a bottle of whine, then it sounds great.