Is the HAL rewritten at this point? (asked in blissful ignorance)
If it's the same machine, and you purely changed the boot.ini, then the HAL will essentially be the same. It's unrelated to the boot.ini.
The HAL is "rewritten" to a greater or lesser extent whenever you plug in any plug & pray device anyway. It's not necessarily a singular entity anyway, more a collection of device drivers written with standard interfaces.
I still think it's daft.
The OS "thinks" it is on an IDE drive
No it doesn't. PnP deals with that on first boot (if it actually needs to).