The way I see it, I already have my stem flipped up, so I was going to install the extension then flip the stem so the rise is negative and go from there. Do you think this will work ok?

I was planing on using a yard stick placed on my saddle pointing forward to gage the relative movement up of the bars.

Next question. Why do the manufactures cut these stems short so you have to add things to them if you want your bars a little higher? Why not just cut the stear tube long and allow the new owner to move the stem up and down untill he finds the sweet spot then have the shop cut the stear tube down if you want?

This is my first real road bike and I guess I'm still looking for the most comfortable spot. I'm making 30-40 mile rides on it now but in the drops I'm just a little pinched around the middle.