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ducatiman is the pro carb guy here.
In general, stock carbs run very well and don't need modifications... IF they're truly clean and the rubber parts and in good condition.
You would benefit from going back to the stock intake system. Again, it's well designed and doesn't need "improvements".
If your valves are out of spec, that will affect the running of the engine, especially when starting and warming up. They shouldn't need adjusting at 4,500 miles, but if there's a chance that it actually has more than that, it would be worth checking. The valve clearance tends to close slowly as the engine wears, and when they get to where they don't close all the way, trouble becomes obvious. A compression test will tell you if they're not fully closing. My 250 was finicky to start and ran poorly when cold. After adjusting the valves it was like I had a new engine.
I've had luck using epoxy to patch small leaks in tanks, but not specifically on a motorcycle. If the hole is above the fuel level it might be patchable. Clean the area with something like lacquer thinner to get any traces of oil and dirt off, and sand the area to rough it up before you apply the epoxy (JB or otherwise).
Until ducatiman shows up, this might be useful:
https://n4mwd.blogspot.com/2013/10/s...-passages.html
Welcome to the board, Alex!