You will notice in this article that the fuel lines were changed from the beginning to the end of the article; that was done as part of this process - if you want more information on this procedure, see How to replace your fuel lines.
IMPORTANT: It should be obvious, but working with the fuel system will expose you to fuel and fuel vapors, which are flammable/explosive. There should be no sources of ignition (cigarettes, pilot flames, sparks, etc) anywhere in your work area, and there should be good ventilation at all times.
1. First, we need to remove the fuel from the fuel line. Turn the fuel petcock to "ON".
2. Start the motorcycle normally, and establish a fast idle.
3. While the motorcycle is running, turn the fuel petcock to "OFF".
4. After 30 seconds or so, loosen the clamp fastening the fuel line to the petcock.
5. Pull the clamp down on the fuel line to free the hose barb on the petcock.
6. Gently twist and pull the fuel line off the petcock.
7. Hold the fuel line up so as to not spill any fuel that may be remaining in it, and to keep fuel in the filter. Hold the fuel line in this position until the engine stalls from fuel exhaustion. Turn the ignition key off. At this point, the fuel lines and filter should no longer have fuel in them.
8. Remove the crankcase vent clamp and hose from the crankcase, to facilitate access to the fuel filter.
9. Loosen and remove the clamp on the left (input) pump line.
10. Gently twist and pull the left (input) fuel line from the fuel pump.
11. Looking in from the right side of the motorcycle, you will see a nut holding the fuel filter assembly to the tab on the front of the fuel tank. Using a socket extension, loosen and remove this fuel filter retention nut.
13. Push the fuel filter to the left side of the motorcycle to free the stud from the frame, then gently remove the fuel filter assembly to the right.
14. Remove the screw holding the fuel filter mounting bracket to the fuel filter, then remove the bracket.
15. Remove both of the fuel line clamps holding the fuel lines to the filter.
17. OEM Honda replacement fuel filters can be found for $18 from Cyclemax Ohio. Until recently, I used Emgo fuel filters, which were a perfect replacement for the Honda filters, and were available for just a few dollars. However, as detailed in this thread about Emgo fuel filter failures, they have had serious quality control problems of late, and some resellers have reported that they have stopped making them. An acceptable replacement is the the NAPA model 3011 fuel filter, which can be had for a few dollars.
18. A benefit of the NAPA 3011 fuel filter is that it has a transparent case, which allows you to view the condition of the filter media, and to check for rust, sediment or debris.
19. The NAPA 3011 filter is slightly larger in diameter than the OEM filter. To get it to fit, partially tighten the bracket screw, and then insert the filter into the bracket until it is firm. Then tighten the screw a half-turn or so to secure the filter. Don't tighten it too much, so that the filter won't be damaged.
20. Because the screw won't be completely tightened, add a drop of blue Loctite to the screw threads, to prevent it from backing out.
30. Assemble the remaining two hoses onto either end of the fuel filter, then tighten a clamp over each end.
31. Push the fuel filter/hose assembly through the middle of the motorcycle, ensuring the filter is pointing the correct direction (in the case of the NAPA filter, the narrow side of the filter is the input side, and should be connected to the fuel petcock). Slide a clamp around the hose connector on that side, and push the hose onto the petcock barb. Tighten the clamp in place. Ensure the worm tab of the clamp (if any) does not interfere with the operation of the petcock.
32. Put a clamp over the remaining hose, then push it onto the barb of the input side of the fuel pump and tighten it in place.
33. Push the stud of the fuel filter bracket through the hole in the fuel tank tab, and tighten the nut over the stud. I recommend you use a drop or two of blue Loctite to fasten this nut in place - I have had this nut come loose due to vibration, even when tightened properly.
34. Replace the crankcase ventilation hose on the crankcase, and fasten its clamp in place.
35. Turn the fuel petcock on and check for leaks.
36. If you have installed the transparent NAPA 3011 filter, you will be able to see it fill with fuel.
37. Start the engine and allow it to run normally for a few minutes, checking for fuel leaks. Stop the engine, allow it to sit, and check again for leaks.
Important!
The fuel system on your bike is the most dangerous system on which to work! Most people take gasoline for granted. We use it every day in our cars and bikes, without a thought as to just how flammable and explosive it is, and just how much potential energy it contains.
It's extremely important that you double check all the fuel line fasteners you loosen or remove when working on the fuel system. When you're finished, go over the whole system, starting from the fuel petcock, and ending up at the carburetors, and ensure each fuel line is pushed completely onto its fitting, that the fasteners are in the correct place, and that the fasteners are tight and in good condition.
This is the result of a GL1000 owner who had a loose fuel line fastener remaining after working on their fuel system - don't let this happen to you!
YOU ALL ARE JUST TO GREAT FOR WORDS 
