I don't think you're stupid at all. I don't know about GNU fdisk, but BSD fdisk can write the MBR. Sounds to me like you accidently wrote over the MBR when you wrote the new partition table.
Another possibility is that you didn't set the Windows bootloader partition to the active partition.
GNU fdisk does not, by default, write the MBR. I made plenty of changes to the partition table before Windows stopped working. Part of my issue in the final stage may have been that the CD I used was corrupted, so it may have claimed to write the partition table correctly but not actually have done so. I didn't get far enough through an install without having every process fail, so that's what I am suspecting happened. And then when Windows did not boot up, I jumped onto an Ubuntu livecd and used ms-sys to repair the Windows 7 MBR, but the SATA hard drive controller had been unloaded at that point. Even when I forced the driver, Windows did not recognize what I was doing. In the end, because it just made lots of sense, I reformatted everything. It works. Slackware is set up exactly as I would have a Gentoo system set up with none of the hassle (all the old stuff was kind of my fault), Windows works just fine with LILO, and life is good.