How do I fill out form 5329, Line 3? Line 1 total from IRA; Line 2 is Code 03 for Disabled.

If your entire distribution was a result of a total and permanent disability then line 3 should be zero.  Line 1 is the amount of your IRA distribution.  Line 2 is the amount that is not subject to the additional tax (10%).  Subtract Line 2 from Line 1, which totals zero if all of your distribution is due to being disabled.