OK in order of your questions. The last day is usually slow, Braided lots of sand bars to avoid. Although in May even at the end of the month flow should be in the 1,000s. If in fact it is around 2- 3,000 you won't have any issues. Motors are a little difficult considering the size of the river. When the water is low, You will never be able to use it to get out.
Prepare for rain. If you wish to get a permit for the left side, You need to hurry. You get that through the Navajo Nation, And it takes them a while to put it together(about a month). Snowpack in the San Juan mountains is good.