On the Clarion head unit. On the plus side it is a marine unit and will resist water damage better than a car unit. I have one in my X-2 and it works fine. It may not be the best if you are a real high end stereo guy or gal (I am not). I would say the remote is REALLY convenient when driving the boat and I think it is a great feature. Whatever you get, try to get something with a usable remote that does not require you to open the glove box to operate.
Also think about using sattelite radio or an all digital i-Pod (the mini or nano not the hard drive versions) for your music as my unit does not do so well with CD's after only a year of use. I think the constant vibrations from the boat just do not do well with moving parts (CD's or hard drives).
As for tower speakers. I have the Skylon Defcon III's (4 6.5 inch speakers with tweeters) and they work fine, good sound but not as good (or loud) as the Defcon V's, NVS Addictions or the new big Skylon Rubicon speakers. I think, but am not sure, that if you tried to fit six speakers (like the Defcon V's) on the 04 tower you would get a lot of sway in the tower and might have to duck under the speakers to get around the boat which would be a pain. If I had it to do over again I would probably get two NVS Addictions. They might be a little more heavy but you could probably slip through in the middle without hitting your head and they would be plenty loud from what I hear. Also remember to check the price of the amp to drive your tower speaker selection. Really big, high RMS speakers need a pretty expensive amp to get the right sound ($500 - $1200).
As for total set up on my X-2. I used to have a single Boss 600W max (likely 300W RMS total to all channels) amp that used to run my tower speakers and a Boss 700W max amp that ran both my Clarion marine sub and the clarion boat speakers. This created a problem, the amp that powered the boat speakers and the sub was underpowered for the sub and overpowered for the boat speakers. Bottom line, little to no bass with crappy sounding boat speakers. I did not do the install but am fixing it as follows. 3 amps, mono for the sub, two channel for the tower and old two channel for the boat.
1. Rockford Fosgate 3001 (150W RMS single channel at 4 ohms) for my Clarion Sub. Much improved bass over my old setup. Clarion sub says 300W max at 4 ohm so I figured 150W RMS would be about right. Note the Clarion stuff does not seem to list RMS for its speakers and this is annoying when trying to match a good amp to the sub or speakers.
2. Rockfor Fosgate 6002 (300W per channel @ 2 ohms X 2 channels) for my Defcon III tower speakers (rated 300W per side at 2 ohms). Note that the amp matches the speaker rating, I hope this is loud and will keep the speakers from having problems again. One of my speakers is at Skylon for repairs, not sure why, could be the cheap amp.
3 Using the old 2 channel 700W Boss amp for my 4 Clarion boat speakers. The boat speaker are now loud and clear but have no bass as I have to set the amp up to high pass to get any real volume.
I am also installing on-off switches between the head unit "amp power on" line to each amp separately. This way I can turn off the sub and boat speaker amps and leave the tower speaker amp on when pulling a rider who wants the music as loud as it can get without blasting everyone out in the boat.
Hope this helps.
Disclaimer: I reallly am not a stereo expert by any stretchof the imagination. Just telling you what I did.