
That is a lot of questions. Not stupid to ask. But go slow amigo. I strongly suggest you get these mods going one at a time and make sure they work before you tear everything up and wonder where it all went wrong! That said, the vibrato mod is a good place to start. And once it works, yes, with a 3pdt you can add two LEDs or a bi-color LED to show the status. First get the mod working though!
No part numbers on this schematic. But it looks like you have the correct resistor circled for the vibrato mod. You will see a 22k and 33k attached to pin one of the IC1 (a 4558.) That looks like the one you circled. Remove it carefully (how carefule are you? how sure are you about the temperature of your iron? Do you have delicate tools to pull it out? Have you looked at a video or 3 about removing components w/o lifting traces on the board?), and put it on a switch, as I said, using an unused terminal to hold one end. Try that out first before you get deeper.
CLR is "current limiting resistor." An Led hooked up to a 9v battery will flash and burn out pronto. There is a limit to how much current they can take. The long answer is spec sheets, ohms law, blah blah blah. The short answer is 1k us pretty safe for most LEDs with 9v. You are probably not getting that much from the LFO, but I would start there. With LEDs like you want to add to the vibrato mod, you will go to 9v and then you will need an R between 4.7k (the default value on old schematics with old fashioned LEDs and over 10k (a go to for modern super brights.)
But wait and think about all that. Maybe the whole project just needs one bi-color LED; it flashed with the LFO and changes color with the Vibrato/Chorus switch. Just a thought. Other wise you have a bypass LED, a LFO LED, and a mode LED.
I won't go into the depth pot mod yet. It involves removing two Rs and replacing with a pot. The Tonepad schematic shows that.