There are some problems that might arise with your plan..

1st, are your sure it is beneficial to take out the heatpipe and replace it with another heatsink with fan? Why don't you just salvage some 80mm or 120mm fans and put it on top of the heatsink to help with the heat dissipation..

Secondly, voiding your warranty is it worth to throw out the window of the 2-3 years warranty??

just put the fan airflow blowing downwards towards the heatsink...kawtim