Hi letsfly, and welcome to AF
If the motivation is to get 2.3, my first thought is to ask whether there is a 2.3 custom ROM for the Merge? If so you could install that without having to unroot.
Otherwise, in general you can return HTC phones to stock using a "ROM Update Utility", which is how you install the factory ROM. Download the RUU, which is a windows executable, to a PC. Boot the phone into fastboot mode (boot while pressing the "back" button down), connect to the PC via usb, run the RUU .exe and do what it says. It should work if the only changes you've made are to root or load a custom ROM.
The catch: I don't know whether people do this with the Merge, but on my phone (Desire) some people (myself included) use a custom HBOOT to change the internal storage partitions (shrink the system partition, giving mor space for user apps and data). If you've done something like this (and since you are S-Off that might be possible) then you'd need to undo it before running the RUU, or else the phone will not boot afterwards (as the /system partition may be too small for the HTC ROM).
Since a RUU is a ROM Upgrade
Utility, it will not run if the hboot you have is newer than the one contained in the RUU package. Unfortunately I don't know the Merge at all, so can't help with finding an appropriate RUU. I also don't know anything about how a Merge gains S-Off, so don't know whether this affects anything in this process.
Final note: running an RUU wipes the phone, so back up anything important before doing this. And remember that after running it you will not be rooted, so won't be able to restore a Titanium backup unless you can root it again afterwards.
Hope something here helps.