Not so much a problem, but an upgrade
The upgrade went almost without a hitch. I think the guide could be expanded though to go beyond "assemble in reverse", as this is rarely the case! This is one of those cases.
Take your time. Don't be rushed. But try to go start to finish in one shot so it's all fresh in your mind.
If you've removed the screws for your heat sink to reapply GOOD thermal compound (vs the crap that Apple poorly applies), make sure that if you put the screws with the springs under them in at say 10in/lbs, that you only put the screws that hold the fan down in at half that! Otherwise the next time you go to pull the fan out, you'll take the heatsink screw with it. Ask me how I know. ;)