Never heard of vradero 1000. Do you have a picture of the side cases of that bike. Even if the side cases fit, the racks might cause a problem, unless you can fabricate them..
Can't help you but I do agree with Whitey here. Then bags may be the same but the racks could very well be a different story. You could find a definate answer to this by doing a little research. Doesn't matter what brand name you search so long as when you do the comparisons, the brand stays the same. Search the parts sites for these bags for both the vradero and the 6th gen VFR. You can do the same for a few different makes of bags. Now check the part number for the racks. If the part number for the two different bike's racks are the same, then you have your answer. I just did an install of the 2003 bags onto my 2006 and it was a bit of a chore. I don't know is it was because the passenger foot peg bracket on my bike was bent a bit, or it was just the nature of the beast. But they eventually did go on. Your comparison is a different story though.
I thinks it the nature of the beast, I just installed some on my '08 and they were a bitch to get lined up.
What I ended up doing is putting all the bolts in only enough to let the threads catch. Then once they were all caught, I tightened them up good which brought everything into place. There is one spot though, where the rack is uncomfortably close to the rear fender cowls. I will have to take another look at that cause I think it will rub if ridden on any type of rough road.
When I installed mine, I had trouble aligning the bolts on the top(grab rail). I had all the bolts in before I started tightening everything else, but when I started tightening the top ones, it was pretty hard..
Sorry but I think the Official side cases for the Varadero are slightly different. Whether this involves physical differences or is simply a matter of styling to match the rest of the bike is not clear. Inevitably you will have to make you own decision on this. However I suggest you try ringing a honda parts department and asking for advice, as they will have the technical fiche for older models. There is an online Honda website showing all their currently available motorbike accessories for European motorbikes at this link Honda Accessories Car and Motorcycle They no longer show parts for the 2003 vtec model but I think the official Honda pannier carrier was the same for all the vtec models - as you will see they still list panniers for the later VFR 800 model as follows. Candy Glory Red - 08L52-MCW-891 Pearl Sunbeam White - 08L52-MCW-8B1 Sword Silver Metallic - 08L52-MCW-8A1 As for the Varadero (VL1000V) they list two sizes of pannier - 29 litres and 36 litres whilst Honda only ever offered 36 litre panniers for the VFR vtec. For the varadero the 36 litres parts are shown below Pearl Concourse Black - 08L52-MBT-870A Shasta White - 08L52-MBT-8B0A As you can see the part numbers and colours are definitely different and the fact the basic part number is not the same suggests they may have some physical differences. Looking at the pictures fo the two panniers on the website suggests the pannier shape is slightly different. Hope that helps