EDIT: @julian's advice makes what I've suggested below obsolete. Not sure how my eyes have never caught that Matched Pairs has the Set Alpha Level option as well. Ignore the rest of this post!
-----
Kudos to Jed's solution for creating the mean difference graph with custom confidence limits. If you're not strictly tied to the specific output of Matched Pairs, I'll add that you can do a paired t-test in Fit Y by X, too, and there you can specify different confidence intervals without needing to go out to Distribution or elsewhere. (But you'll still need Jed's method for creating the mean difference graph if that's what you're after.)
First get your data into tall format as required by Fit Y by X. Starting with your data in wide format (required by Matched Pairs), add a column with a unique ID for each row to specify your blocks, then use Tables > Stack to get to tall format. In Fit Y by X, enter your blocking variable into the Block role in the launch dialog. Click OK, then select Means/ANOVA/Pooled t from the red triangle, and you'll get the same paired t-test you get in Matched Pairs. You can change the alpha level under the red triangle, and the confidence intervals in the report will update.
I've attached a version of Jed's data set in tall format, with a table script that runs the paired t-test in Fit Y by X and uses 90% confidence intervals.
Ross Metusalem
JMP Academic Ambassador