hmm my masters was easy compared to my phd, now that i am looking back at it! or maybe i am looking back with tinted rose glasses! the writing of the Msc thesis of the 3 month project was stressful though! i can't even remember exactly what the heck i did! or what the project was, something about cloning.
my advice though, is to write as you go along, those 3 months that you spend doing your final experiment project, do fly by, and you don't want the stress of writing your MSc thesis, whilst embarking on a phd. and don't worry if the experiment doesn't pan out, or you get negative results. Msc examiners aren't so fussy as long as you write a nice story.