My guess that the CD player and speakers are the most responsible for the lack of clarity, but improving the CD player will probably be less expensive and more likely to be a change for the positive than changing the speakers.
The reason I say this is that speakers are such a matter of personal taste that, if you're happy in all other respects, changing to a completely different speaker is quite a risk. You might gain clarity but lose other aspects that you like.
I own a Marantz CD67SE and a CD5000 and both err on the warm/fuzzy side of neutral, largely due to high jitter on the DAC clock.
You could switch the CD player for an Arcam, or perhaps the Cyrus CD player here on Agon, or you could add a reclocking DAC such as the Benchmark DAC1 to sharpen up the source end of things.
If you wish to change speakers I think you could do much worse than a pair of Green Mountain Audio Europas. Like the Vandys these are 1st order coherent designs, so they excel in imaging and a broad soundstage, but they are extremely clear speakers .... occasionally ruthlessly so. They remind me somewhat of studio monitoring with Acoustic Energy AE1s .... they are very neutral.
