Fuel filter is buried inside the lower tank (under the seat). To get to it, you need to have an empty upper tank and as little fuel as possible in the lower. You need to buy the rubber gasket, new fuel joining pipe between the upper and lower tanks, along with the extremely strong, sprung hose clips. Oh and a new filter. Info is in section 5, page 56 in my workshop manual. Other manuals vary though.
It happens after an hour ? Is that related to the level of the fuel in the tank or not ? Is your coolant OK - replaced recently and topped up - it could be heat related ?
You say you have only ridden for 40 km since you got it ? Is that correct, or is it a typo ? What was done before you got the bike, or is that unknown.
Anyway, if you think its a long time since the plugs and air filter were done, I would start with the plugs and the air filter. Give it a treat and put some good quality fully synth oil (check the rating for your temperature in Alberta) The Honda manuals are inconsistent in what they recommend, but there is a good diagram to show the range for 10W-30 and 10w-40 oils - and a new oil filter (Make sure you follow the guidelines in the owners manual for the spec of the oil). And then run through a couple of tanks with some better quality fuel (preferably not with ethanol - I find it makes the engine knock more readily) and put some fuel injector cleaner in the fuel for a couple of tanks.
Try to have a long run, letting the engine spin up (as a police bike instructor once described it to me) - ie keep the revs up higher than you would normally, and if you can arrange for it to be with 'thick air' - cloud cover, early morning or later evening - that helps too. He told me to ride it in the 4000 to 5000 range for a while. I did this on the way home from spending a 2 day training course with him - after an hour the engine felt loose, easy to rev and responsive.
The pre-2008 models seem to run leaner, or the engine management system isn't as good as the models since 2008. And this is going to sound odd, but it comes from a long time ST1300 rider and senior employee with UK Honda - and it seems to work.
He said that if the bike is happily coasting along and there is very little change in the demand on the engine, then the engine management system seems stop monitoring everything as frequently. To wake it up, it needs some serious input - changes of revs.
Now - whether or not this is true, I do not know, but I had a problem with my A6 which used to seem to stutter after riding on long open roads. Nothing doing much and then I'd want to accelerate away from a corner, and the power wasn't there.
A few hard blips on the throttle and all was OK. In fact I kept the high revs up for a few seconds while pulling the clutch. And the problem would go away. I wondered if this was similar to the diagnostic test mentioned in the manual where it was necessary to run the engine at high-ish revs for a short while before doing a test. I know I have read it , but can't find it at the moment. 10 secs at 4000rpm rings a bell, but I wouldn't rely on that. Someone on here will know for sure.