I know everyone is trying to be helpful, but SOOOOO much misinformation here! I'm all about tech and learning, so lets put these misnomers to rest so that it won't keep getting regurgitated in our echo Spyder chamber?
The length of the spring has zero effect on the ride or rate. Its already been pointed out that the installed spring is a linear rate, so unless it is too long and binding at full compression OR unloading and unseating at full droop....That isn't your issue. There is no difference in the rate between a longer/shorter spring. The block height of your installed spring is 2.46" so you have 3.54" of available compression travel before it binds. IF your total shock stroke is only 2.5", that leaves room for 1.04" of preload, but I wouldn't push it that far......... Just do the math to see IF the spring is binding. IF the spring has enough travel in the shorter configuration, it's lighter and therefore marginally cheaper/better overall?
To expand on the spring rate thing..........It is common practice in the off road world to run springs WAY over length so that they can install a lighter spring rate, dial in A LOT of preload. This nets the desired vehicle ride height, a lower ride frequency, slower ramp up of spring rate, while stuffing the wheel quicker into a hole (due to higher wheel rate at droop) after a bump event so that the tire maintains traction to control the vehicle and keep putting power down....Think miles of 3' deep whoops where the tires just move up/down nonstop. The downside is this can introduce unwanted body roll,acceleration squat, and braking dive. This is similar in theory to how Baja Ron's JRIs are configured? I'd quote the numbers between JRI/Baja Ron's and Elka for comparison, but the numbers are no longer shared for the JRi's......... From memory, JRi's have a much lighter rate than Elka, but this makes sense when Ron is setting them up with his complementing sway bars kits for a more compliant ride and controlled roll. Now keep in mind I HAVE NOT sampled Ron's shocks, but we do have his "Ultra Bar" on the RT.......So I guess it speculative, but I have 35 years in the suspension industry and can imagine the scenario.....Because of the bar, I opted to drop one front spring rate from what Elka supplied.
As far as the actual rate is concerned, I would guess that a 500# would be in the ballpark considering you don't have the aux bag......I don't own an F3, but IF the motion ratio of the rear suspension is the same as the RT (mounting points and swing arm length), you are right where I would think is good. I felt a 475# resulted in a ride frequency that was too low for our taste even with the air bag active. I swapped it to a 600# and it's MUCH better for the heavier RT that we run loaded most of the time, but possibly a little too "sporty" for one up riding if you want a marshmallow ride like stock.....It's awesome for traveling with a light load or even 2 up once the bag compensates. Eibach probably isn't going to help you decide.....They don't offer off the shelf Spyder applications.
What you really need to do is put a new bolt, reinstall, and take static and rider sag measurements.......Lots of tutorials on the net. Then you will have an idea of what you need. Yours is easy without dealing with the air bag.
Can you post up a pic of the lower shock mounting hardware? The OEM shock had one full length steel sleeve with plastic spacers over the top on each side to keep it centered sandwiched into the swingarm mount? If Sharcus just supplied some spacer to stack the width, this is why your bolt is bending. FYI......You could never bend upward that bolt by jacking under it unless the bike weighed 1000's of lbs.
You might also want to add an outer shock protector sleeve before you reinstall to keep the grit from blasting the shaft and force feeding the seal pack. Cheap insurance on ScAmazon.
Anyway that was a lot..........