Hi, and welcome. I did a very quick search but couldn't find an online version of the owners handbook. Perhaps get in touch with Watsonian Squire and see if they'll send you one?
Regarding the list of niggles - well, yes..... I know what you mean. But the fuel tank is offset I'm told because it wouldn't fit straight on with the new fuel pump etc in the way. Mine's the same and I've added it to the list of endearing charms of the bike.... That tool box grommet is prone to get pushed through and out back when you replace the cover, so when you replace it, put your hand behind to hold it in place. My pipe started to discolour rear of the heatshield after around 1500 miles. Heatshield flew off last week and hasn't been seen since. Check all nuts and bolts for tightness regularly, particularly after a good thrash! I found the gearbox takes a bit of practice, but I came to the bike after a forty year break from two wheels. Mostly positive and smooth gearshifts now.
The other stuff you mention does sound unlucky. At least there's a long warranty. Don't forget, these bikes are made by hand using only stone tools and glue. But they do ride lovely.