Count me among those . . . swapped mine during the Covid lockdown in '20, was great to have something to do whilst stuck at home.
Main things I can think of
* 5th gen engine bolts right in to the 5th gen frame - no mods needed.
* The "cushion" (Honda's term - I would call it "swing arm mount") that connects the swingarm to the engine is different - requires a 6th gen version to mount to the engine
* Yes, the swingarms are slightly different
* 5th gen uses remote coils with HT leads, 6 gen is 3 wire COP setup. This is the BIG thing to contend with in doing a swap. I retained COPs. Alternative is to source 5th gen harness and ECU and swap all that over.
* 6th gen rads are larger, IIRC 2 additional rows
* 5th gen cylinder heads are about 1 1/2" shorter - creates no issues
* Shorter heads mean that the cam timing marks no longer appear through the inspection hole in the 6th gen frame (most people don't know why that hole is there). Makes valve
adjustments more difficult. Suggest checking valves prior to doing swap
* Despite cylinder head differences, throttle bodies are a direct swap
* Hoses, thermostat, everything cooling system is interchangeable
* If keeping 6th gen electronics, you WILL need a VTEC solenoid connected to the harness or you will get a no-start
* 5th gen has a smaller alternator than 03 and up 6th gens. Currently swapping a 6th gen alternator over.
* Despite all the similarities in the engine block, water pump, etc, 5 & 6 G alternator covers are different and do not interchange.
* As mentioned above 4th through 6th gen gear ratios are different. The 5th gen is under-driven by 1 additional tooth, makes for about 200 rpm or so increase at 70 mph cruise. Barely noticeable.
* Power output is indistinguishable. Honda did not add VTEC for power, torque or any other discernable butt-dyno reason. Maybe emissions, marketing, or who knows why. I don't miss it, and I do NOT miss the insanely difficult valve adjustments on the VTEC - the main reason I swapped it out.
* Despite keeping 6th gen electronics, there is no VTEC "hit or kick" . There is a subtle change going through 6,800, but if no one knew about it, they would have no idea - nothing like it is stock.
* Wheels and front rotors are interchangeable.
* 6th gen brake system has 2 proportioning control valves vs 5th gen 1 - bleeding procedure is similar, but different. The linked brakes are plumbed differently between the 2.
* 6th gen has available factory luggage
* I have seen 6th gen tanks swapped to a 5th gen - doable but requires trimming the 5th gen bodywork in the front where it curves around the tank
* 6th gen has available ABS. I've read that about 10% came with ABS, but I know of no documentation of that. On 1 occasion I was glad to have ABS, for me a good addition.
* 5th gen has more room under the seat.
That's probably more than anyone wants to hear. Owning both, I don't note much difference between them. And now, having one swapped, there's even less. If it weren't for ABS and the factory luggage for long-haul riding, I would probably stick with the 5th gen. However parts are getting harder to find for them, so I don't know how much longer they will be practical for daily or long trip riding. There are still times when I start the 6th gen that I just look at it and still can't get used to hearing that whine from the cams. For my $, that was the best engine Honda ever did or will make. I'm super happy with it.