Word pretends to be able to do fancy layouts but if youre creating stuff for publication then it always better to use some other software (I spent a lot of time tweaking the graphics on research papers to get them through academic publisher requirements). I found one way was to import the document into MS Publisher which will allow you to go up to 11 dpi then set the resolution for each graphic element. But that doesn always work and Publisher is (deservedly) not installed by many nowadays as being mostly useless. Never had problems with the Adobe Acrobat - Word plugin unless something had been done (filter shadow etc) to the vector object in Word and then the effect and the vector is rasterised. Transparency is always a bit hit-and-miss but I found that creating a backboard made things better (large rectangle the size of the page with the fill and surrounds in white and sent to the bottom of all the pages objects). Or using Inkscape I would re-check each vector item just to make sure that it was still a vector save them as eps files then use Publisher for layout. Basically it all a faff and you finally realise there a reason for Adobe Illustrator - it creates perfect PDF.