As to changing all three holes at 5K IMHO its not needed so I guess you could call it over kill, however my thoughts are like you said it is easy to do when you are changing the oil. It adds a very little time to the job and not much cost as you are only out a qt of primary and trans fluid.

The filter funnel works well but still be prepared with some rags, if you are doing this in your garage I would suggest a big piece of cardboard under the bike just to keep any drips off the floor.

Go ahead and change the O-Rings on the drain bolts each time for new ones. IMHO they are to cheap to risk using an old one that may be nicked or flattened. I think the O-Rings are a couple bucks at HD and can be found in bulk for cheap on Amazon from several sources. Here is 100 for for about 16 bucks
Get an oil filter with a nut on the end like the poster above linked to. He linked to a K&N and there are a couple of others that make a HD replacement filter with a nut as well. IMHO having a filter with a nut on the end is much easier to remove in tight spaces than trying to use a filter wrench that can spin or crush and overtight filter.

As far as torque wrench for the spokes I have never owned one. To be honest have never had much of an issue with spokes getting loose on HD wheels. I tap them with a screwdriver or spoke wrench and listen to the tone. As mentioned above a nice "ting" and I consider it good a dull sound and I tighten it up till it rings the tone of the others. My son raced MX for 15 years which can be hell on wheels/spokes and I used the same method on his wheels.

 

I've been changing all my oils in my all my Harley's for over 42 years now and have never used any special funnel. Just put a piece of cardboard under your bike. The next day or two keep another piece of cardboard to catch any remaining drops.
The primary takes only 38 oz of oil (on my bike), no filter, is easy to change.
You be surprised how much crud is stuck to the magnetic drain plug after just 3000 miles. Compensating sprockets and clutch hub bearings are expensive to repair, I'd change the oil. (I'm still running the stock compensator on my Ultra Limited that I bought in 2009).
The transmission takes one quart, (again no filter) and again you'll be surprised how much metal is stuck to the magnetic drain plug on new unbroken in bikes. On my 2010 I changed mine at 1K miles, 5K miles, 10K miles, then every 10K miles after that. Transmission repairs are really, really expensive to repair.
Buying a couple of quarts of oil every 3 or 5,000 miles is a lot less expensive than the repair cost. And once you do the oil changes the first time it's no big deal after that.

 

You can find the o-ring at McMaster -Carr. #13, about a nickel apiece.

https://www.mcmaster.com/#o-rings/=17r2t5e

Probably can get the same thing at a Fastenal store near you.

 

I change my oil every 5000, trans and primary at 10000. Get the oil filter socket wrench. made the oil filter drip catcher out of a soda bottle. And with spokes I always used the old tap with a screwdriver method, after a bit you know how they are supposed to sound.
If you see a grease fitting, grease it.
Do you have bike jack?? If so get your tires off the ground and spin them, listen for any out of the ordinary noise. Going into my neighborhood it is a slight downhill, straight , for almost a 1/4 mile, I ride at night, so coming in to be nice to my neighbors, I'll hit the kill switch and coast a couple hundred yards at about 25mph, good time to listen for bearings and any other non-engine noises.
Put a wrench to whatever bolts you see and make sure they are tight.
Give the bike a walk-around and check lights, blinkers, brakes and tire pressure.
Get the manual.
Working on these bikes ain't really hard.

 

5k service at the local dealer here is a little over $200. My indy did it for the same a little less with synthetic in all 3. I like having the receipt for warranty purposes plus they check a whole bunch of little stuff. I'm no stranger to working on them as I did everything on my last one including rebuilding the top end but I want the paper trail on this one at least until the warranty runs out.

 

One dealer on Long Island whacks you for $500 for the 5K Service and charges extra $$ if you want synthetics. I have a manual and will be doing it myself.

Just rediculous.....

 

With a manual you will have no problems. I change oil every 5k and primary every 10k.

 

I received the service manual today. Good thing because I thought the transmission drain plug was the oil drain. Lol!! Still waiting on other items I ordered on line, but I definitely am confident now I can do just about anything needed. Thanks for the wealth if information posted.

 

This may also help. :-)

 

I just wanted to add that the total cost for me doing a all 3 oil change myself, buying the filter online from JP Cycles, one quart of Redline shockproof for the tranny, a jug of Mobil One at Walmart and 2 quarts of good quality clutch specific 20-50w oil for the primary is about $60.