Will a 08 motor bolt into a 04 readily?

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@Ionbeam = Wasn't the gearing change done via final drive changes, rather than trans changes?

The water connections are the main thing I'm suspicious about. I'd bet the motor mounts are the same. No reason to change them. But with the Gen II's dual fans and different radiator, hose route changes could have occured. That might be as simple as swapping some fittings from the Gen I to the Gen II motor though.

The fuel rail is likely an easy swap. Bore spacing has not changed between Gens. Personally, I'd prefer to swap just the fuel rail and leave the Gen I TBs with the trashed motor. A lot of crud has run though them, even if they are fairly bullet proof by themselves. Perhaps use the newer injectors with the old fuel rail?

Another salvage yard issue is motors being left outside. This seems to happen far more often than you would expect. Between impound yards where the bikes sat, then the salvage yard, there can be significant corrosion and weather issues. Ask all the questions you can and get more detailed pics of the motor before buying.

I was lucky and got a low mile motor from a forum member that had low sided and then bought back the wreck. Well documented and a fantastic quality seller. No problems so far after 20k on the new to me motor.

 
@Ionbeam = Wasn't the gearing change done via final drive changes, rather than trans changes?
The fuel rail is likely an easy swap. Bore spacing has not changed between Gens. Personally, I'd prefer to swap just the fuel rail and leave the Gen I TBs with the trashed motor. A lot of crud has run though them, even if they are fairly bullet proof by themselves. Perhaps use the newer injectors with the old fuel rail?
You are correct, the gearing change was done with the secondary gear, the transmission gearing remains the same. Disregard my previous note about gearing.

I do believe that the clutch slave cylinder and/or push rod is different on the Gen II. Either the master cylinder or the slave cylinder can be swapped to fix the problem. IMO, I would put the Gen I slave cylinder into the Gen II engine.

The fuel injection system is very different from Gen I to Gen II and it involves different fuel pump, different fuel rail, different electrical harness, different number of engine sensors and a different ECU. A Gen I for Gen II ECU swap would be virtually impossible due to changes in the ABS system and the meter assembly. IMO animal should stick with a straight Gen I FI system.

I do believe that the VSS from the Gen I can be swapped into a Gen II. At least the early Gen IIs simply had a cover over the VSS port in the engine case.

Putting a Gen II engine into a Gen I frame is the wicked hard way to get a high output stator ;)

 
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Wow! I can't thank everyone enough, this is super. I have found a ebay 05 GEN-1 motor from Boise that comes with f.i., ecu, ect. After everyones help on this forum we have decided to go with a GEN-1 motor! It will make our lives a LOT simpler. I will definately compression check the engine when it arrives and have the valves adjusted if it's good. We will also use the f.i. from the new motor and anything else we can as it supposedly has 9k on it. The insight provided by relaying the conversations with the mechanic in Casa Grande that worked on the bike were awesome! Only on the internet. I leave tomarrow to get the bike that is being brought up to Flagstaff. The guy says he WILL get another FJR as soon as he gets on his feet. Bet he switches from car to bike oil and remembers to have the valves adjusted. Thanks again

 
Grumpy in Hendersonville NC has an '04 motor for sale. He had a slide down in the rain that ruined a lot of tupperware, forks and subframe. I think the motor is completely untouched. It had high output stator already installed.

Shoot him a PM before you risk Ebay. He's a known good.

 
Skooter my good friend, I could kick you in the butt right now. This would have made a perfect donor bike for my electric commuter vehicle!

Animalrooster: If you decide against the project, let me know! Otherwise, good luck!

 
FWIW I have a perfect '05 wiring harnes and ECU for a non ABS bike. If you need either I'm sure we can work something out.

 
I'd be willing to bet that between the two engines, and some transferring of ancillary components, the 08 motor will fit just fine.
I've looked into this. Gen I bikes have a VSS. Gen II do not, but there is a plug for it at the back. I don't know if the internals are there to trigger the VSS though. Everything else will fit. You just have to use all the Gen I FI and wiring and mounts from the motor. As far as the gear selector sensor on the Gen II, you just don't hook it up.

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