If it's new hardware, your best option is a fresh build, IMO. You really don't want to even attempt to copy a server build; even though SIDGen might be good at rebuilding the SID, you'll be in trouble with hardware drivers from day one until the day you give in and rebuild.
If all the servers are identical then this should be as simple as building one, installing all apps, then using your favourite imaging software (Ghost, Altiris, etc) to create the rest, lastly installing MetaFrame on the freshly imaged servers - all of which can be scripted and done in unattended mode. Better still than installing the apps with the server images, use IM, SMS or some other scripted application packaging method.
Since these are application servers, user data shouldn't be affected. If users are storing data locally on your current MetaFrame servers, then it's time to re-think the architecture and use policies to store data elsewhere.
If you're running MetaFrame XP, this is all very straightforward, as you can build the servers and add them to your existing farm, then decommission existing servers once your test cycle has completed.
Never underestimate the usefulness of an extended test period, or proper planning.
I know this is a bit generic, but I know nothing of the size of your Citrix farm or the hardware or software involved.
Hope this helps