I've posted my experience permanently rooting the Evo Shift 4G. It's not for the light of heart, it voids your warranty, and a couple people here will yell at me for it. On the other hand, it breaks out of the locks HTC put on the phone: You can remove Carrier IQ (HTC's Spyware preinstalled), Nascar, NFL, Sprint TV, etc - whatever you want to do, you can finally do it.
Get your patience hat on and have at it!
This may not have worked for me but AT LEAST I HAVE MY PHONE BACK!!!!! I tried this procedure many times but could not get it to work. I believe it is because of a missing file in the hboot eng file. When at the downloading steps I saw that the hboot file was supposed to have two files but only had one. This created problems when trying to unlock the boot loader. After finishing the bootloader steps the super user kept crashing. I gave up, but then I remembered some articles that had a way to lock sense in if you have temp root. After finishing up pushing super user you gain temp root with these steps. If you add in this one last line you can GET SENSE TO STOP RELOADING! Type in "echo ro.HOME_APP_ADJ=1 >/data/local.prop" so far so good. I have been free of this issue for a day.. hopefully it worked and I'm not just jumping the gun Haha
HaLo17, there's actually just the one important file - hboot_eng.nb0. The other file is just the standard hboot in case you want to flash back to the locked hboot for peace of mind. If you look at the instructions, all you do is mount hboot_eng.nb0 in the right place for the device to accept it, flash it, and voila.
It sounds like what you did was flash hboot and stop short of installing a new ROM. You have to go the whole way to installing one like Fresh ROM to get permanent root etc. If you don't want Sense, you can choose another Gingerbread ROM for Shift, that comes without Sense. Fresh ROM uses Sense and is generally as close to the default Sprint install as possible, which for me meant a lot less confusion when trying to figure out what's normal, and what's something going wrong.