Hello my name's Charlie and I'm writing cus my 98 Honda CBR 600f3 wouldn't start. First of all I did a carb cleaning on my carbs and b4 reinstalling I also put new plugs in and after putting it 2getr it ran like a new bike and did for several wks but b4 putting my tank back on I cleaned the old gas out from sitting all winter outside and lost a Allen screw to the gas cap and my dumbass 4got about it and it rained and got water in my gas and ran it not realizing it and it shut off couple miles away from home so got some water remover and cranked and cranked with no luck so I pulled the tank and fuel lines and got any and all I could out and even drained my bowls and put higher grade gas in it in case any water was left in it and after several cranks got nothing and jumped started it cus all the cranking drained my battery but I did get it started and rode it for 20-30mins hoping to get any water in it pushed through and went home shut it off and the next day wouldn't start so I started troubleshooting steps in the book for it and the only thing I could find was the rectifier/regulater not testing right on my multimeter so put a used one on changed my plugs again and put used coils in and still wouldn't start so I drained the gas again and put a new battery in it and finally got it started but my R/R is getting very very hot so I'm wondering what is going on now....Thank you

 

R/R does get very warm. Standard.
Clear the decks with your issues one at a time. You seem to have nearly new plugs with a new battery and access to more than one set of coils and R/R. Your working R/R should have no continuity between cables.
You seem to have drained your fuel plenty of times so your water issue is probably on its way out or gone.
If it’s just a very warm R/R don’t worry.
Clean plugs, good fuel, start her, prove she’s charging, running on all four, and ride her.
Good base readings to have if the issues persists allowing you easier problem solving.
Best of luck mate

 

I'm new to working on bikes so is there something I should start on first and work my way to other areas or is there a certain order I should go in when trying to troubleshoot problems

 

Also when checking testing the RR should the bike be running or in the on position or not running at all and do I check it through the back of the connection that plugs into the RR or unplug the connection and test the tabs on the RR it's self

 

The R/R would probably be best tested off the bike, so no power required ignition off ( it can be done in place ) and tests require your digital multimeter at the block connector.
Just watch one of the “how to’s” on you tube to assist you as it’s very simple. Quicker than me explaining anyway !
As for problem sorting, we all have our different ways of working things out but a manual is always handy, especially for electrical drawings. For me, i do like a mental flow chart away from my issue ( normally ends up like a spiders web with the bike in the middle lol) and start further back making sure it’s good then follow towards my issue. Like I said earlier, good base setting proved, then work towards problem. Difficult to explain really lol.
You’ll crack it.....best of luck mate