Rode it home yesterday... 485 Mile trip.
One thing I don't like so far if the linked brakes... Any way to unlink them? I think I like to have control of my own brakes.
You probably have it in the default high linked mode. You can change it to the low (lesser linked) mode which is much better. No, they can't be turned off. Lots and lots of threads about it.
Also, I think the bike is lower? Where do I look to see if he installed the lowering links?
It is more likely a seat and/or handlebar riser you are not used to. But if it is lowered, then it has a lowering link or they messed with the suspension. If the front is lowered, the tubes would obviously be protruding from the triple tree- and that is not possible without risers. If the rear is lowered, there would be a lowering link right smack in the middle of the bike on the very bottom, around the center stand. With adjustable links, the center stand has to be removed completely. With fixed links, the center stand will remain. And if it was properly lowered, then the stock side stand will not work, the bike will not lean enough to stay on the stand, so look for a replacement side stand, too.
And id they are installed, and problems I can expect? Handling , etc? I also ride mostly 2 up.
If they lowered the rear and did not lower the front by the same amount, or vice versa, yeah, it is going to suck (because that is the wrong way to do it). Otherwise, I don't think it will affect handling all THAT much if it is done right... but there are some differences. And, of course, there is less clearance.