Fuel filter orientation is as per the schematic for the pipework that Mr G kindly referenced from a post I put up some time ago.
But here it is again if you can't find it:
If the bike has been stood around for as long as you say, my advice would be to also look at the vacuum fuel pump as the insides of mine had definitely seen better days before Ethanol took it's toll but luckily it's rebuildable.
Also worth a look is the vaccum fuel tap, which unfortunately isn't rebuildable but doesn't cost a fortune either- about £35 I am guessing.
Going on from those if you haven't done so already, would be to replace both vacuum pipes from the inlet manifolds as any air getting in will stop things operating as they should.
Like I said before, I did the lot when I went through mine as it was getting on for twenty years old and I didn't want to keep having issues- so far I haven't and so the time and money spent back then was all worth it not to keep getting interrupted with similar issues.