The short answer is yes. Anything you do will affect clutching. The longer answer... Let me start by saying there are a lot of others on ths site who are much more of an expert with clutches than I am. That being said, here's my 2 cents worth.
By lowering your gearing (numerically increasing your gear ratio), you are reducing the load on the engine for a given RPM, speed, loading condition. Basically you are using a slightly lower gear. In theory, this would decrease your top speed. I have read many times on this site and others that the yamaha's are geared too tall from the factory anyhow. I.E. the engine (stock) doesn't have enough power to have the secondary fully shift out under normal riding conditions. By gearing down, you can potentially fully shift out your secondary clutch. My simple answer is gear it down and you'll be just fine. Watch your Maximum RPM. There is a lot of fine tuning you can do with both the primary and secondary if you're looking for every last ounce of performance but unless you're racing, you'll probablly never notice the difference. I generally use the factory clutching and jetting recommendations from the manual for my sled. I went with a taller gear ratio, but I am running a much longer track. I also like to think of it this way, by gearing down a little I am decreasing clutch temperature slightly, all else being equal. Keep in mind, with your drop and rolled chain case, the gear/chain chart is no good. Meaning you probably have a longer chain for a given gear combination than what is listed in the manual. Just count the links on your existing chain, and look at the chart, specifically where a change in ratio dictates a change in chain length. Just use the same increase or decrease at those jump points. Also, the chart I attached earlier is for factory gearing available. You can get smaller top gears and larger bottom gears from aftermarket suppliers such as Hartman. if you look at the gear chain chart, there is not an option for a 19/42 combination, yet that is what I and others are running.
In summary, if you drop 1-3 teeth on top or increase 1-3 on the bottom, I would think you'll run just fine without messing with clutching. Sorry about the long winded answer.