Ok, guys. I just finally mashed my feeble monkeybrain into shape over this one, so I thought I'd share.
For ANYONE still getting the "FAILED: (remove:90 hboot pre-update! please flush image again immediately)" error on windows, here's an updated batch file. It's attached below, just extract it into your r6-desire-root folder and try running it again.
For those interested, the problem is you need a wait - and I saw some people posting revised batch files with a 'sleep 15' in there earlier in the thread. Sleep is not a batch command, at least not anymore. The workaround is ping yourself for fifteen seconds before a retry - I'm not making this s*** up. But anyway, there you go.
Edit: Oh yeah, almost forgot - I'm finally on a vanilla HTC rom with decent headphone volume (that's all I've been doing this for - thanks T-Mobile! I need to void the warrenty to listen to music, smart move), so thank you everyone involved, you've made my day. Cheers, guys. step1_windows.zip