Like Albino said, you should be able to FTP the contents of the HeXEn disc to your HDD and run it from there.

Do not delete the softmod until the flash is finished. When the flash is done, it will shut off the Xbox. After that, you should turn your Xbox back on and launch HeXEn from the HDD again and unlock your HDD, so you can put it in another Xbox later if you ever need to. The softmod does not actually cause any conflict with the new BIOS, but if you still want to remove it (I always do because I don't like having useless files sitting around), you can use the clean C partition function in HeXEn to delete Rocky5's softmod, or just manually delete his "Dashboard" file from your C partition.

HeXEn installs the UnleashX dashboard prior to the flash, so you will still have UnleashX, but it's now located in E:\Dash\UnleashX, has a different config than the one from Rocky5's softmod and doesn't include Rocky5's custom skin. You can easily just add those in though.

Of the two BIOSes you listed, I have used iND-BiOS 5004.67 on all of my Xboxes and they can run without a DVD drive.