Froyo 2.2 SU Permissions issue (tried everything!!)

I want to start out saying you guys are all amazing and have helped me out a million times in the past. Although I've never posted here...I usually I find help by searching around. Also I'm sure you all have heard this question a million times but I have searched high and low for an answer, not just here but all over, and still nothing can fix it. So here it goes and please don't flame!
So I installed the 2.2 froyo update on my droid (which was not rooted before this). I downloaded the update from engadget followed one of the thousand walkthroughs to install and went great. I used SPrecovery with the update.zip file, of course allowed the update and such. Installed the froyo update, reboooted and everything works great except one problem. Any of the rooted apps (ex: setcpu, rom manager ect...) says cannot find root access (or something of that extent.) Also I have re done the update.zip file about 5 or 6 times now and still nothing. The superuser permissions app is there and has always been there but I do not get the box asking to allow permissions. So I can't run any rooted apps!
Things I've done:
Master clear/reset. Second, third attempts to root with sprecovery(also cleared cache).
Su commands in adb with android sdk.
Reinstalled all apps pertaining to this problem countless times.
Enabled debugging.

I'm very fimiliar with iphone jailbreaking (been doing it since 1.0 os) and with that changing permissions to 755 fixes it, but I'm still pretty new to this but it sounds to me like I missed a step somewhere. I'm 99.9 percent sure its rooted because some apps tell me it is and SU is there. I've givin up on this one so any help you guys could throw my way would be great!
Thanks again.

 

So is the update.zip file you directed me to the sprecovery deal? In which case I already have that. I'm reading now about mount/remount rw commands. I did none of that haha. Is this the part I'm missing? And can I do it from my phone? And how do I do that part? Thank you so much for the help by the way haha. This has been a nightmare
Also I'm messing around with droidroothelper V0.5 and still no su. Or maybe what do I do from there to get su?