I only know the answers to a few of your questions, a little more info could help as well.
The CEL is probably due to the exup servo motor being removed, unfortunatly if it has been then its likely that you need to plug one in, reset ECU to turn it off, and plug in one of the few servo eliminators options, which could be home made(7-10k ohm .25 watt resistor) and once done that you could leave it off for good.
LED's do indeed cause the faster blink rate, no the rate will not increase with the fronts being changed. you have 2 options for the flasher rate, 1st being an elecronic flasher module that doesn't rely on the resistance of the lights, meaning they will work with proper timing regardless of light style.
2nd option is wiring resistors inline with the led's which i wouldnt recommend, cause i believe the light output of the led's would be slightly less and its more work.
In diagnostics mode you can see the rpm's but there is no setting or way too see them while riding the bike, as far as i know.
lots of people use the sandman and its probably the best one there is cause the others dont protect the case from the chain if it were to snap.
There are 2 products that correct the speedo, the speedo drd and the speedo healer, the drd is tiny and takes water like a champ the healer didnt like water so much last i checked but a condom would probably work lol. A gps would work as well... thing is people say you cant correct the odo and the speedo at the same time, which i still dont understand, unless its the 8% difference you mentioned, either way its not a big deal for most .