Hey Dave,
That's one tough ride to cut across to Marsabit from Omorate solo, we went straight down to Loyangalani. I'm not sure what Omorate-North Horr-Marsabit section of road is exactly like but I wouldn't think that it would be any better than the Moyale-Marsabit road. I know the road to Loyangalani wasn't

.
In regards to the west side of Lake Turkhana, I have met one biker that did it but that was years ago and most are put off by the hassle and uncertainty of negotiating with the boat owners to ferry your bike across the river in their canoes. One pedal biker I met had a tough negotiation to get them down to even a bearable price. The roads are supposedly somewhat better on that side though.
As for the African west coast roads, depends on the season and route but in general they aren't that much worse that what you have already been through if you stick to the main route. I just came up from South Africa to Nigeria and while there is definitely more bad road than the east coast, I'm not sure that it is enough to need to switch to a different bike. I was riding a DL1000, which also falls into what I would consider the category of street orientated dual sports, and has about the same clearance as yours and while at times I wished I had a bike that was more dirt orientated, in general it was perfectly fine.
As a side note, I also met a rider from the UK in DRC who had completed a RTW the year before on a new Tenere but had heard that the roads were rough on the African west coast and as such went really light and bought a slightly older XT for a trip down to SA. In short, he didn't find the roads nearly as bad as expected and wished he had brought his other bike which he had already put the time and effort into setting up.
Sorry to hear that your bike has given you some trouble thus far but sounds like you now know your bike inside and out. Knowing the weaks spots of the bike you are riding (and all bikes have weak spots) is probably one of the most important things. Your bike already has the dents and scratches of the road so isn't really going to depreciate much more. Once you factor in the cost of shipping your bike home ($1,000-$1,250) and the depreciation on any different bike that you buy, (and other small items like the costs of temporary import permits at some borders if you don't get a new carnet), it'll cost you a fair bit to switch and I'm not sure that the roads really require it. For the incremental cost vs. benefit, it's probably very debatable.
Anyways, just my two cents. Drop me a line when you are heading north and maybe see you somewhere on the road.