The trip went off with a few minor hitches- I figured I'd post here so people can learn from our experiences/mistakes.
1) Definitely bring spares, especially a spare prop. for a few reasons.
The first reason was the rangers were all over us, and likely wouldn't have let it go without. That goes double for the registration. They hemmed and haw'd about the temp tag, but the senior ranger was aware enough to know the laws and just warned me to make sure I didn't show with a temp tag next time. They went so far as to check the rating on the fire extinguisher I brought (it needs to be a class B), inquire about spares and tools. I had a pretty extensive tool kit, the printed owner's manual, spare shear pins, and a spare impeller (for the water cooling of the motor) a quart of oil in case it got submerged, spare cordage for the pull start, frame nuts and bolts, etc. .
The second reason was as I was adjusting the transom height at the put in to make sure we had the prop in the water, I took it off, set it on a pelican case, it fell off and broke the prop. So instantly, the spare became the primary. The plus side is it made us figure out how to change the prop in an easy place, and made us super vigilant about depth the rest of the trip.
Shortly after we got it running started and running, it died, and the pull cord broke getting it started. Luckily that also was a pretty easy fix done under way (with some serious emphasis on 'don't drop ANYTHING') and we were together and motoring about 15 min later.
2) 3.5 hp 4 stroke did ok.
We were not the fastest barge out there, but we were making between 5 and 7 mph depending on current with a 13.5', 18', 14', mini me, shredder, aire couch, paddle boards and tubes rafted together. (see video). We motored from put in to the doll's house, and from the last rapid to Dirty Devil. There were a couple long days, but we all were praising the motor often because of wind. It was also pretty quiet. Sitting right next to it and steering made it hard to hear much else, but a bit away on the barge, conversation was fine.
3) Bring extra gas.
After reading on here, and doing some math, I estimated needing 2.5 gallons, so I doubled it and brought 5. This was pretty much exactly what we used for the motoring described above. PaulK (having been on a motorless trip in the past and ended up rowing 'till 2 am the last day because of wind from the sound of it) added another 5 gallons. We didn't open that can, and put all that gas into the vehicle at the end. That said, the mental safety net of having that extra can made us far more comfortable with motoring as much as we did.
4) Don't leave it on the mount in the rapids.
For the rapids, we put a trash bag on the motor head, tilted the motor forward , secured it with the pin, the triple rigged it with cams and cordage to make sure if it fell off it would stay out of the water. We also pulled the prop off and put it in the tool kit. After big drop 1 we noticed it wasn't sitting like it used to, and a quick look showed we broke the mount. The mount is cast aluminum, and sheared off at the securing pin. After re-rigging it onto its side in the 18'er we went on through the rest of the rapids of the day. Inspection at camp showed it would be a relatively easy fix with a cam strap, and the only function lost would be the ability to tilt up if the water got shallow.
For day two, we rigged it sideways on the back (stowed according to the manual) and it fared very well, to the point where it started first pull when it was time.
As for rigging it, I had some spare frame parts from a while back, so I made an add on to the frame. It had an adjustable transom height made from 1" HDPE and extruded aluminum stiffeners, and places for two 2.5 gallon gas cans. The adjustability proved key for setup, as the initial guesses were done with the stern of the boat hanging off the trailer. I didn't really get pictures of it in action, but this one probably shows it best (keep your eyes on the motor!