I did the headwaters 2 summers ago.(June 19-26, 2003) It's a good trip in terms of scenery and wilderness experience. However, it's not all that in terms of whitewater. That said here's the details. Start hiking when the river is 1800cfs and falling. Much higher and things could be really exciting on the first day of paddling.(although it would be better for the run as a whole, the steepest sections would most likely be to high for most boaters) * This is the best whitewater of the trip.IMO The Forks are a good run but at the flow you will be doing the Headwaters they are boring. By the time we got down there it was about 1000cfs. The Forks are great above 2000 but much lower and well you get the picture. So here we go. We used Golden Trout Packstation. The owner is Dan Shew. They will carry kayaks but are a bit pricey. They as well as the rest of the packers in the Sierra are part of the Sierra Maffia. Get any price quotes in writting if you can. They increased our price by $100 per person when we arrived. Unfortunately there was nothing we could do but pay the money or carry our boats and gear ourselves. So we paid the man and set out on our way. We chose to hike in from the bottom instead of going over Shepards Pass for a couple of reasons. One there was still a lot of snow. Two the packer was not sure he could get up to Junction Meadow since the trail crew had not been through. Luckly for us we knew people on the crew and they made sure the packer would get through. Otherwise he would have dropped our gear and boats at the point in which he would have been stopped. We didn't want to hike over the pass to find that our boats were not there and have to walk downstream in search of them. On the short the hike from the bottom (Lewis Meadow/Jerky Meadow) is about 42.5 miles. We did it over 3 days. (It's more of a stroll than a hike as there is only one significant hill to climb around the Kern Lake area) Camping at Grasshopper Flat the 1st night and Kern Hotsprings the 2nd night. We averaged something like 14 miles per day. The Hotsprings is the highlight of the trip and by hiking in from the bottom you can take advantage of it twice. Once hiking in and again at the end of your first day of paddling. The hike is spectacular in it's own right and worth doing even if not boating. The second day of paddling would take you from the hotspring to somewhere around the Kern Ranger station/Kern Lake most of which is flatwater and log jams. The next day would be from Kern Lake down to Painter's Camp/The Hazards. This section starts off good through Grasshopper Flat then mellows to class 2/3 with a few good rapids here and there. The next day could be the last through the Forks down to Johnsondale Bridge. We took a couple of layover days to hang out and watch the Wide World of Worlds but you could do the trip in 4 days. A strong class 3/4 paddler could do this trip(at the described level) if you took your time and walked a few small sections. Drop me an email if you have any other questions. Later
oh and the 90 some odd mile thing your thinking about isn't possible as well as the few sections below Johnsondale. There is just not enough water in the river at the time you can paddle the Headwaters to also be able to do these sections.(actually you could get down them but it would be less the ideal) And typically the Cataracts does not run until July/August when they release water out of Lake Isabella. Sorry to burst your bubble.
One more thing. The High Sierra hike goes over Shepard's Pass not through the Whitney Portal! Although you could go this way you would need special permits to go over the Portal and the hike would absolutely SUCK! In fact either way (Shepards or Whitney) would make the Upper Cherry hike seem like a senior citizens walk.
* If I were to go back I would probably start hiking at something like 2200cfs and then just hang at the hotspring if the top section was to high for my liking.