factory reset is taking you to recovery,because,well,thats what it does. normally the stock recovery would take over,and wipe certain areas of the phone whenthis option is selected. since you have amon installed in place of stock,its logical that this option takes you now to amon.
if youve installed miui,you may need to install a matching kernel,or you can restore your nandroid backup(you did make one,right?) if the stock kernel is still on your phone,as long as you didnt wipe boot with amon ra.
search xda for a stock rom that matches whatever software you were on prior to starting this. if you dont know your previous sw version,check hboot: 2.27.0000=newest sw of 4.03.605.2 and 2.25.0000=previous version of 3.14.605.12
in a worse case,you can relock your bootloader(fastboot oem lock
in a cmd window,with the phone in FASTBOOT),and then run an ruu.
.zip files should be placed on the root of the sd card(use a card reader) and renamed to PH98IMG,then installed in hboot. .exe files are run on the pc,just follow the on screen directions. start the utility with the phone in fastboot.
after youre back to a working phone,you might check out these links:
Scottys noob friendly root guide-start to finish
s-on and want to flash roms? READ THIS
also,youll need to flash superuser in recovery,you cant just install it from the market. the superSU file i recomend is linked in the first link.
as you can see from the second link,i strongly recomend to launch recovery into memory with the rezound,it makes things a bunch easier.
holler if you have more questions