I'll try to give you the answers as I remember them...not had any coffee this am
so doing this off the top of my head!
re the fuel filter - nope - you cant clean it. the filter on the 650 isnt just a filter...its a filter and a gas tank pressure regulator. if you have a look at the BMW price for the stock item you'll see that its a dam site more than just a filter. its actually a sealed cylindrical component.
as far as the injectors go - the best way to clean them - if you really think that they are that bad...is to find someone local, take them the injector and get them to clean it. this shouldnt be too difficult as a high % of vehicles in Peru are diesels and every diesel vehicle is injected. they should therefore know what they are doing...infact simon had this done with his injectors in Arequipa in Peru. cost well under $10 to do both. good job done.
from memory the off the shelf, pour in your gas tank home-style injector cleaner solutions will most likely not work on your bikes injectors as the chemical solvant in the solution requires a specific amount of heat to activate it. and the injectors on bikes are placed diferently than on cars. dont get as hot and therefore the solution cleaner just ends up being squirted out and being burnt up as your engine ticks over.
as tomtten mentioned altitude can play a part - so have a look at your altitude.
things that I would try if I were you are:
check the terminals onto the battery for corrosion and make sure they are done up tight.
check your spark plugs are seated properly and are gapped correctly and still looking healthy
check your air filter - try starting it in the morning with no air filter in and see how it acts.
another thing to consider - your throttle sensor can easlily get itself out of whack - especially if you are going from road to dirt from crawling around town at slow speeds. this problem can start with the symptons you have described and get progressively worse. to reset the throttle sensor is easy.
turn your ignition on.
turn your throttle all the way to max...and then release it quickly.
do this twice more. (total 3 times)
turn ignition off.
wait 15 secs
its now reset to factory default.
its always worth considering that you may have condensation/water in your gas tank..or just a bad batch of fuel.
check your oil level hasnt for some bizzare reason suddenly dropped. (bike gremlins do exist)
let me know if any of this helps!
just a quick point - after over 150,000 miles I have never had to clean my injectors. I have just put in a new set but that was as a precaution and not a necessity. so your problem may lie elsewhere.....