I'd start afresh and shout it new sprockets and chain, along with all the normal maintenance items, fluids, plugs, air filter, oil and filter etc. I'd also dive into the electrics, solder up all the grounds in the dreaded orange earth block, solder the stator lead wires to the R/R and its output connector, upgrade the R/R if needed and make good the Main Fuse B 30amp fuse holder and wiring.
I did most of this last winter, just after I got the bike, also went through the front end ( bushings, dust seals, rotors pads ) and settled on Race tech springs and rates suggested by the Capt. ( one of the best things I could have done, what a difference in the front end ) also tore down the motor to the cams and checked all the valves, surprised to find they were within spec, removed the PAIR system while I was in there, rebuilt the clutch slave cylinder and flushed all the old brake fluid
out ( clutch and brakes ), had the injection system cleaned and replaced all the water cooling hard line O rings etc., surprised how bad they were, also new thermostat, I would never have guessed it by running the motor but the old one was stick wide open, new coolant, plugs etc
This winter I want to check out and update the rear systems such as chains and sprockets, I doubt I will pull the rear axle system as it rotates fine for chain adjustments and the bearings seem good
I like to think I have had a lot of different bikes over the years but this 99 is better feeling than even the 90 VFR750 I have, a keeper for sure