[Sidecar Bob]

Note that the rubber pieces around the spark plug caps that sit against the tops of the valve covers are only intended to keep debris out, not water. The drain holes (circled in red in the pic below, courtesy of motofaction.org) allow any water that runs into the spark plug wells to run out.
Note also that in theory the engine should run normally even if the drain hole is blocked and the plug well full of water BUT if the boot that seals the spark plug cap to the spark plug is missing, damaged or has just hardened enough that it no longer seals properly even the normal amount of water that runs into there when it rains can get into the cap and short the spark.

 

[Sidecar Bob]

The rubber boots just pop off of the ends of the plastic part of the cap but unfortunately they aren't available separately.
Fortunately the whole cap assembly is available, both the original NGK ones and aftermarket copies.

 

[Sidecar Bob]

Your 650 came with both resistor caps and resistor plugs and it will work just fine with both. As I understand it some resistance between the coil's secondary winding and the spark plug's gap increases the duration of the spark event for more efficient burning of the fuel/air mixture (= more power for less fuel).

The "brass rod mod" has nothing to do with performance (except that something that actually runs is obviously performing better than something that won't run). It is merely a way to keep the bike running if one or both of the resistors is corroded too bad to clean up or otherwise damaged and can't be used.

As Mike said, if your caps read 5000 ohms you shouldn't need to replace them.
Unless you find that water is shorting the spark when it rains or something like that. I wouldn't rush to get new caps until I knew that was a problem; With the plug well drain open you may find that the water doesn't get into the cap enough to cause problems.

I have an IR non contact thermometer but I seldom use it for things like that, simply because I don't need it very often and if I leave the battery in it will kill the battery in a couple of weeks so by the time I get it out and put the battery in I can put my hand near each of the headers and see if one isn't hot (I don't have to do that very often).
The key is to put your hand near the header, not on it.

I think the only time I needed to know the actual temperature of the outside of anything on a bike was when I was figuring out if the Rust-Oleum Hammered black paint would work on valve covers (it does and it holds up pretty well).

 

[Sidecar Bob]

Yep, squirting a bit of water on a bike header will tell you if it is hot too, but you have to get something with water in it to use.....
With only 2 headers it is easier to just feel the heat.

Re spark plug wires, I remember a co-worker back in the '70s whose car was hard to start on damp days. Another co-worker opened its hood to see if he could help one really foggy day and we all saw a light show ;-)

BTW: Speaking of spark plug wires and resistors it is usually advised not to use resistor spark plug wire (basically carbon impregnated string) on bikes because it doesn't last. If/when you need to replace the wires you should be able to find 7mm solid copper core plug wire at a small engine repair place.