Welcome to the forum and welcome to the world of antique vehicle ownership (they own us, not the other way around). Your bike is about 4 decades old and from the sound of things has not had all of the maintenance necessary to keep it safe & reliable (not to mention some possibly questionable modifications) so it is highly recommended to go through the Factory Shop Manual and perform all of the service procedures, regardless of whether your bike has reached the specified mileage.
I also recommend looking on all rubber parts with suspicion because rubber does not age gracefully. Check the date codes on your tires and replace them if they are over 5 years old no matter how good they look & feel (old rubber simply cannot flow around the irregularities in the asphalt well enough to grip, especially if it is cool or wet). If your bike still has the original rubber brake line(s) (should be replaced every 2 or 3 fluid changes = 5 or 6 years) I recommend shopping for modern stainless braided ones (they last practically forever and double the life of the fluid). And don't forget things like the rad hoses and the boot between the engine and swingarm (they can crack on the bottom where you don't see it).
I hope you are aware that all of the modifications you listed will affect the function of the motorcycle. Did the Previous Owner give you the required safety certificate and UVIP?
I can't say for the ones CMSNL sells but there are a lot of aftermarket intake manifolds for sale that don't come close to fitting properly.
I bought large self adhesive heat shrink tubing on eBay a few years ago for something else. It was much less expensive than places like McMaster-Carr but it takes a lot longer to get to this part of the world (I've recently learned that Aliexpress often has lower prices than eBay plus faster shipping).
Note that Room Temperature Vulcanizing ("RTV") can refer to any rubberlike material that does not require heat to cure. What you got is more liklely to be silicone sealant and it would be far from my first choice for that application.
I've had good results using Shoe Goo to patch cracks in intake anifolds.
This plus point #1 indicates that the carbs probably need to be properly cleaned & rebuilt. When you are looking at carb kits remember that the metal parts in aftermarket kits are often so far out of spec that they can cause the bike to run worse than before the rebuild and that the best kit available (the Randakk's Original kit) does not contain any jets, needles &c because Randakk determined that A) Those parts seldom need to be replaced and B) on the rare occasions when they do need to be replaced your local Honda dealer is the best source for ones that do meet spec.
This (plus the condition of the carbs) indicates that the person who modified your bike was more interested in style than in function (anyone who really knew what they were doing would have dealt with these things first, then used the bike for a while and made changes based on what it actually needed in order to better do what they wanted it to) I would consider everything they did to be suspect because people like that often make fundamental errors that can seriously affect safety.
I highly recommend going over everything they did thoroughly, especially any welds they did but also I would seriously consider replacing any bolts they used to attach things instead of welding because they may have been over tightened and weakened.
You may find this an interesting read
Hi All, I'm new to the forum. Hopefully you guys go easy on me if I missed some introduction thread of some sort. I purchased a Thompson Rebuild done by a guy named John Thompson in Michigan. I'm guessing he is known on this forum? It was a bike he just completed about 6 months ago...
www.cx500forum.com
See Bahn's comments. It really doesn't make sense to go through all of the effort & expense to open the engine for the sale of a 50 cent o-ring but make sure you remember to replace it if/when you have the engine apart for something else.
FWIW, mine has had silicone sealant to seal the camchain tensioner adjuster bolt for several years and will continue to until the engine is apart for something else.
As for the other possible leaks, "there's no point fixing what ain't broke". My advice would be to clean it thoroughly and coat the parts of the engine you suspect are leaking with a fine powder (talcum, flour, anything fine that will cling to the surfaces will do), then go around the block a couple of times, let it cool down and look for tracks in the powder that will lead you to where the actual leaks are (it might even turn out to be only 1 leak plus oil blown to other areas while riding).
