You might start by doing an exhaustive search to see if any known construction mistakes could cause you major headaches. Here's an example from a different upgrade (eSata) on a different Mac model (Pro): ...
Apple has fouled up in terms of making the memory bay mounting screws almost unremovable by using Loctite in the wrong place, effectively welding the screws to the standoffs they mate with ...
http://www.xlr8yourmac.com/feedback/mac_pro_ext_sata_case_kit.htmlAnd perhaps you should double-check that instructions cover actual upgrade on the actual model you plan to upgrade. Here's an example for CPU: ...
With the switch to the Intel Core Solo and Duo line, Apple uses a socketed CPU in the Mac Mini which allows the processor to be replaced. With the 2009 model they switched to a new glue process which does not allow for an easy upgrade ...
http://en.wikipedia.org/wiki/Mac_MiniI'm not sure how difficult the putty-knife case-opening is: it might require disciplined gently-persistent force and patience. Here's another option:
http://headwedge.com/wordpress/2006/11/01/mac-hack001-opening-mac-mini-wire-method/