1.) How big is your printer? To tell the difference between a 1Ds3 and a theoretically perfect camera will take a very large print. I'd guess that a 1Ds3 will saturate even a 17" printer (no way to tell the 1Ds3 from any possible "better" camera on a 16x24 from a normal viewing distance). The difference will start to become apparent with a 24" printer, but that is a floorstanding beast.
2.) Are you willing to wait 6 months for what Canon comes out with next? Nikon's (24.6 mp, but image quality that is even higher than that pixel count suggests) D3x has substantially better image quality than the 1Ds3 (especially if you're willing to use the 14-bit mode which slows the D3x down to 1.5 fps). Canon will replace the 3 year old 1Ds3 sometime in the next 6 months, and they will need to beat the (already 2 year old) D3x. I predict somewhere around 30-32 mp, with a full-speed (5 fps) 14 bit mode and the dynamic range of a D3x (which is as good as any but the very best medium format). Because of diffraction and antialiasing filters, that won't be QUITE the image quality of a 31 mp MF system, but it'll be right in between the D3x and 31 mp MF. The D3x already makes stunning 24x36 inch prints, so the new Canon almost certainly will as well (with the right lenses, a caveat that applies to any of the top "35mm" type cameras). At that point, you'd need a 44" printer the size of an upright piano to make a print that shows the difference between the "1Ds4" and medium format. There's at least one reasonably priced (by these rarified standards) 44" printer out there - Canon's own iPF 8300. I just bought one (haven't even gotten it fully set up yet), and the one big caveat is that the darned thing is literally the size and weight of a very ugly piano. Coming from a 24" printer, I was very surprised at how huge the 8300 is - I knew it was 6 feet long, but I had NO idea just how squat, stocky and sturdy it was. If you want a printer like that, it goes in its own room (fortunately, I have a spare bedroom it can live in)!
Unless you are willing to make the commitment to a 44" printer, the "1Ds4" will be plenty of camera for almost any purpose (and will have truly superb AF tracking). Even with a 44" printer, it should do pretty darned well. Note that a 40x60" print is so large that you can't easily mat around it - it has to be framed without border because mat board only gets to 40x60" (until you get to really odd stuff). Even with a 44" printer and a lot of landscapes that lend themselves to big prints, I'm sure that less than 10% of my printing will be 30x45, 36x54 and 40x60, simply due to the handling problems. My bread and butter print sizes will be 12x18, 16x24 and 24x36, any of which a "1Ds4" will handle just fine (I bought the big printer mostly for the ink cost savings, and only secondarily for the maximum print size, although 24x36 canvas wraps (which need extra image size) are a nice capability to have).