Sounds like a good plan! This is only your second quilt, and look what you've learned already!!!
Here's a tutorial on checking that seam:
http://www.quiltingboard.com/t-89997-1.htm
Once you have figured out where that pesky scant 1/4" is on your machine, your blocks will fit much better. For me the time I take to make sure I hit the seam allowance is offset by the time I save not trimming blocks and/or trying to ease mismatched blocks to fit.