Mac Mini (intel) freezes after Security Update

On May 16th I downloaded and installed ´Security Update 2006-003 (Intel)´ on my Mac Mini. Since then I have been unable to have any other session with it than in "safe boot" mode.
Then, on May 18th, during one of these "safe" sessions, I also downloaded and tried to install ´Mac Mini SMC Firmware Update´, hoping that this could be the resolve. The initial behaviour changed slightly, but that was all.
When I now look for upgrades, I get the message that the latter is available for download, so it has obviously not been activated.
I have been keeping the ´box´on for days in case there was some process going on in the background that would resolve it, but in vain.
As something appears to have entered the machine with these updates, are there any way to reverse them and throw them out?
Mac Mini   Mac OS X (10.4.6)  
Mac Mini   Mac OS X (10.4.6)  

Thanks for your reply!
To adress your questions in sequence:
1 - After powering up, the grey Apple screen emerges, and shortly after the rotating wheel of bars starts going. Then the screen changes to blue, and the shield showing "Starting Mac OS X" has its blue ribbon rotating up towards 100%. Now, here things may change from time to time, sometimes it reaches 100%, sometimes not. But the next phase is the same; a shift to a dull blue-gray screen with nothing on it, which remains until I eventually give in and presses the power off button for some seconds. I even left it like this this for a day, to make sure nothing was going on behind, but in vain.
2 - I am not sure about your meaning "Since the computer operates normally in Safe mode....", I did not normally operate it in safe mode, it became a necessity after the download I mentioned. Tried to look in the suggested FAQ, but did not find anything I found relevant. (But then -being new to Macs - maybe I did just not understand it?)
3 - The Security update was the last of 7 updates that was downloaded from the Apple Support pages, the others being: QuickTime v7.1, Front Row Update v1.1.2, iDVD Update v.6.0.2, iWeb Update v1.1, iPhoto Update v6.0.3 and iMovie HD Update 6.0.2. As I said, I am new to the Apple structure, so I do not know if these softwares are regarded as third-party or not.
There is, however, as far as I can see, nothing that indicates that any type of panic with the core is declared during start-up, it just becomes incommunicado!
4 - Obviously, the most attractive option I can see is to follow your advices here. But the mentioning of specific versions of CD in conjunction with re-installatin alerts me somewhat. What I got with my Mac Mini are two CDs; ´Mac OS X Install Disc 1´ (Labelled Mac mini) and ´Mac OS X Install Disc 2´. Does this means that I am unable to do Archiving?
Finally, I have some other topics (Basically with QuickTime) with this Mac Mini as well, that was the reason I started looking for updates in the first place, that will become important again when I overcome this blow. But as I am looking around in the forums I become increasingly aware that there are lots of people experiencing similar problems to myself (Poor functioning of Airport, problems using flat-screens as monitor), and now this one. I mean to see a pattern, and that is that there are significant differences in functionallity between OS X for the "normal" processor and the one for Intel. How deep goes this difference? There is obviously softwares for OS X that cannot run on this machine, and how do I keep them out?
Hoping for some more helpful hints
Best Regards,
Ole
Mac Mini   Mac OS X (10.4.6)  

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    The day after I reverted to 10.9 to repair keyboard glitches caused by Security Update 2015-002 (and persistent in Yosemite), Apple released Security Update 2015-004. Such a quick succession of -004 on top of both -002 and -003 was the hint to me that -004 contained fixes to the glitches.
    I crossed my fingers and jumped back on the install-wagon. Yosemite 10.3 completed its second installation and my keyboards/keypads remain functional!

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