I have the 2002 version of your engine. The cap/rotor swap out is easy. I buy NAPA ECH RR207 cap and ECH RR256 rotor. Magnetic screwdriver with Torx bits T15 and T20. Take a Qtip with some grease on the end and extract any pieces of crud that may be blocking the screens while in there.
For starters grease your hinge pins on each side. From the vid I can see yours is old enough to still have the zerks. That may help the trim creak but wouldn't help the steering creak however.
I use a homemade cart not wide enough to accommodate the prop so the prop has to come off for removal and stay off for re-installing. I hand turn the shaft so that the shifter stays in forward. Go slow and make sure it stays that way and lines up properly. Always in forward gear at the helm...
Nauticus Smart Tabs will eliminate a good bit of it for not much money and have other benefits also. There are tons of threads on this site addressing smart tabs. Generally very positive results for inland boaters.
Yes I've wondered about this also. I tighten the hose clamp well and check for leaks frequently. I have enough slack to be able to cut off some hose if needed. But I admit your (and QBhoy's) method sounds appealing.
This is similar to what I do. I use two OMC quick disconnects. One stays on the fogging tank line, just to close it off. Another I carry loose to plug the boats fuel line once removed. I have to remove the panel beside the starboard side of the engine for access. Is it a PITA? Yes, such is...
What's exactly wrong with it? There is a manual for it. Search for Quicksilver Commander 3000 Classic Throttle Control manual. I downloaded one from somewhere, can't remember at present. Used it to replace my thumb switch. Parts seem to be readily available.
If that's a steel frame trailer and the carpet is against the supports consider cutting the new carpet so wet carpet isn't laying against the steel. As you can see mine were getting a good amount of rust/rot. I painted Chassis Saver on them.
Also depends on your situation. If you trailer and launch a lot, launch solo at busy ramps for example as I do, the Keelguard comes in very handy. I consider it one of the best additions I've made to the boat. I try to avoid using it but sometimes it's called into action to get the job done.
Assuming you and your buddy sit in the back, two batteries in the back, gas tank in the back, etc. Guessing you badly need to move weight to the front somehow. 40 horse is not a lot for that rig. Take a look at Nauticus Smart Tabs.