Installing Windows manually Here's the situation:

I've got three partitions on my disk - EFI, OS, and a Data Partition + 40 gigs of free space for a Windows partition. I already deleted the Recovery partition to avoid conflicts in Bootcamp and comply with Windows' 4 partition limitation.

Technically it should work flawlessly, but the Bootcamp Assistant is still having a problem with the current partition table and denies to automate the process. I can create a Windows installation USB drive and download the drivers, but the Assistant won't help me with the rest of the partitioning process.

Now the question is: If I create that bootable Windows setup drive with all the needed drivers via the Bootcamp Assistant and install Windows manually, will this work? I just don't want to cripple the rest of my stuff on that disk and render my Mac unbootable.
What you need is the refit tool.  Then on the Mac (via DiskUtil) shrink/resize your Mac partition and create a partition for Windows in the free space. 

Then, via Refit (on the Refit boot menu under tools), sync the Mac partition table and MBR-partitions (this will create a windows-readable MBR type partition map that matches the partitions you created on the Mac).

Then just boot from a Windows CD and install in the new partition.  Do NOT modify the partitions (adding, removing, etc.) from Windows though.