Be prepared for cold, wet, snow and ice in MT, especially when crossing the passes. We did a loop out of Missoula last year that incorporated a couple of days of the TransAm route. Couple of nights it got down to 40. Had we left Missoula a day earlier than we did, we would have gotten soaked by several inches of cold rain that hit Hamilton. That was late June. The week before we arrived, snow flurries were predicted in some of the places we would be. Leading up the trip I followed a few journals. Couple of people got snowed on. One fellow got caught in a bad storm heading west from Ennis, MT and ended up getting a ride.
Can't speak to OR as I have only ridden in the area the Trans Am uses in early September. However, if you look at something like this, you will see it could be pretty cold at night:
Note that McKenzie Pass west of Sisters will almost certainly not be open when you arrive. It would be a shame to miss it. The landscape at the summit is amazing, and the descent of the west slope is fun if you don't mind switchbacks.