There is a LOT of truth to that comment about the whole being greater than the sum of the parts. The KLR is a good example, as is the Suzuki SV650 naked and S models, especially from 2001 and back. Ask anyone what they liked about the bikes and they have a hard time coming up with anything in particular. They usually just say, "I don't know. There is just something about it..."
I recall my first ride on a KLR. I too had that immediate reaction. I had one shortly after that. I had many great adventures on it. For all of its flaws, there was just something about it that made me want to get out and ride it. I have no doubt you will have a great time with yours as well.
As for the the dealer comments about the Doohickey, I would take that with a grain of salt. BMW would NEVER admit to there being a problem with the final drives on their bikes from 2004 and back. Dealers would act all clueless when presented with a failed drive. And yet, the internet was flooding with people reporting failures. When they moved from the 1150 powered bikes to their 1200s, the final drive got a complete redesign. A selling feature was that it was better than the old and would not suffer the same failures... a back handed admission that there had indeed been a problem. They also mentioned that the new drives were sealed for life, so no more need to change the final drive gear oil as part of the regular maintenance. Well... it did not take long before reports of failures in the new drives started appearing. Then BMW went back to recommended regular gear oil changes and the drives were retrofitted so you could drain and refill the fluid. As always, the dealerships acted clueless about the problems.
I experienced a failure on my 1200 GS that destroyed my final drive. The rear brake rotor mounts failed, ALL OF THEM. The rotor came off and in the process destroyed the final drive. The dealer acted like it was the first time they had ever seen or heard of this happening. I get home and withing two minutes have found multiple threads on various forums discussing this specific issue. Even though the bike was way out of warranty, BMW North America eventually agreed to send me a new final drive. All I had to do was pay the labor for the swap. About six weeks after I got the bike back, BMW issued a recall on the wheel hubs because of this specific failure mode. There were so many bikes affected that they were backed up for about 9 months trying to get all the new hubs manufactured and get all the bikes in for service. They had enough failures to warrant a recall of ALL their bikes with these wheel hubs and yet the dealer expected me to believe he'd never seen or heard of it before... Right
I had a fuel injected VFR 800. When I took it to the dealer for a major service, I asked them to be sure to sync the throttle bodies. The service manager gave me a blank stare in return. I asked if he had a service manual for the bike. He got one out and I showed him where it clearly stated that this procedure was part of that service. He had never seen or heard of it before. FI bikes had been out for about five or six years at that point and this was the first time he'd heard of or seen this!? That did not do much for my confidence in the dealer. When I picked up the bike, things only went down hill from there because they did things I explicitly told them not to do, they did stuff I never asked them to do, and they double charged me for several items. They even removed my brand new front tire, less than 100 miles on it, and replaced it with a different tire just because a tech was gabbing with another guy and left a tire sitting near my bike. The guy working on my bike just saw it and installed it without even checking the work order. Of course they charged full retail and an hour of labor for that! By the time I was done reviewing the work order and the bill, it went from around $1600 to about $800.
Dealers want riders to think they are experts at caring for the bike they sell. I have no doubt that there ARE some dealers out there that really ARE experts. Sadly, they are the exception and not the rule. Thank God for the internet. I cannot imagine how frustrating things must have been in the days before the net. I guess that might have been the reason why there were more actual riding clubs, so riders could pool their knowledge and work on their bikes together
Welcome to the Two Wheeled Texans community! 
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I keeed I keeed.
plenty of clearance, should go anywhere you ask it. Nice bike! Man, that 250 came and went fast.