If you are going to watercool, how are you planning to create the water jackets?  Given the need for precision, that will be the hardest part of the job.  Also, it's not just the heat sinks on the outside of the blades - you will need to include those between them too.  If you can solve the jacket issue, the rest should be fairly easy, as you can probably use off-the-shelf parts.  Don't forget you'll need fans on the rad, so there's no escaping them altogether.

I agree with you regarding the S3 fans - they are very loud indeed.  At least mine are, anyway - perhaps some are less so.  To quieten my S3s down, I decided to change these fans.

The fans are of the PWM 4 pin type, with the speed controlled by the hardware.  It is easy to buy 120mm fans that are much quieter than the standard ones, but it is not so easy finding fans as efficient - the standard ones are very good!  To replace them you need a fan with a high static pressure for the inlet - the best ones I found were the Corsair SP120 PWM High Performance edition fans, designed to push air through heat sinks, etc.  Even a 120 to 140 adaptor with well regarded 140mm PWM fans wasn't as good as these Corsairs.  On the outlet, I eventually settled on the Thermalright TY143 140mm PWM, which has a 120mm mounting.

Note that my S3 fans spin within a range up of to about 2,300 rpm for the inlets, so I chose new fans accordingly.  I have seen some printouts on here showing fan speeds of 5000+ rpm.  If those are accurate speeds (not sure how they can be), I don't know what anyone would buy to replace those (industrial standard fans, perhaps?).

My S3s are now much quieter and very tolerable, for me at least.  BUT - even with these expensive replacement fans, the S3s run a degree or two hotter than the standard ones.  It's a trade off that I'm willing to accept to save my hearing!