I wish I would have seen this a year and a half ago when it was first posted. Still, I'll post an answer in case someone else is searching for a solution.
The easiest way is to open a copy of the document so you don't accidentally make changes to the original. Then double-click one of the equations to open it in MathType. Change the Full size to whatever size text you're using in PPT -- probably something between 24pt and 32pt. (You do this in MathType's Define Sizes dialog -- bottom of the size menu. Set Full to this value, and make sure the next 4 sizes are in % values, not pt values. If they're not in %, set them to these values, respectively: 58, 42, 150, 100.) Before closing Define Sizes, make sure "Use for new equations" is checked. Don't close MathType yet.
If you're using a different font in PPT than you're using in Word, now go to Style/Define in MathType. Change the Primary font to be the PPT font. Close MathType to save that equation in Word.
In Word, go to the MathType tab on the ribbon, look for the Format Equations command, and click it. Set it to use "MathType's 'New Equation' preferences", and "Whole Document". Click OK and wait for it to finish.
Now you can copy & paste equations from Word to PPT and they'll all be the correct size. There's nothing you can do to avoid the issue with the equations not being inline in PPT. PowerPoint doesn't allow any inserted objects to be inline with text.