Brushes - hmmm..well, most folks go for OEM parts whenever they can but if you cannot get Yamaha parts, then the aftermarket brushes seem OK as far as I can tell. Certainly, you need some brushes, and if the ones you get are too short, then get whatever ones you can, with a preference for OEM parts.
The area in and around the carbs and below the fuel tank on an XS650 is waaaayyyy to tight for everything to fit in easily.
Using aftermarket pod air filters may make things easier, but those have their own pitfalls (the K&N pleated ones don’t work well with stock XS650 carbs) and you give up stock appearance - which may or may not matter to you. The upside of pods is that you can ditch the stock airboxes and save some space in that crowded part of the bike. Certainly, a lot of folks use pod air filters of various types but some tuning may be required to get the jetting correct for good operation.
As for fuel filters, generally, a bigger filter is always desirable because it can filter more stuff (Air / fuel / oil / whatever..) before it becomes clogged, but in this case, you want the smallest possible fuel filter simply because it will be easier to fit. I have had good luck with some teeny-tiny little conical units and some folks use little rectangular filters. Anything bigger than the smallest size - will likely be extremely difficult to fit into the available space and you do not want any pinched or sharply kinked hoses.
One trick I have used on my ‘76 Standard (the redoubtable Lucille
) is to feed the LH carb with the RH petcock and
vice versa. That allows the fuel lines to be a little bit longer which helps to fit things in - like fuel filters and the crankcase vents.
I guess your bike, as a later model, will have only
one fuel inlet to feed both carbs (the early bikes had one inlet per carb).
Anyhow, the fact that you are struggling to fit everything in - is no surprise to me.