As the new carby is the OEM one for the Chappy, the factory jetting in it might not be suitable for this particular engine combo.
Yeah try a couple of bigger Pilot jet's, and tune the mixture screw so that it rev's sweet and smooth when you blip the throttle.
Fit the #32.5 pilot and start up the bike (should start easy), and let it warm up for a few minute's.
Then raise the idle speed a couple of hundred rpm's, now adjust the mixture screw in till it start's to stall, and back it back out till it just idle's ok.
Then turn the mixture screw out 1/4 turn at a time, then let the engine settle for around 10 second's, now adjust the mixture screw out again, and let it settle again.
Listen to the way the engine is running, you eventually want it adjusted so that the engine is at the smoothest/highest rpm.
Once you are happy it's pretty close, turn the idle speed screw back out so the rev's drop back to a normal speed, give it a couple of blip's to check it come's back to idle speed ok, and it's not set too low.
Turn the bike off, and screw the mixture screw back in till it start's to nip up, count how many turn's it takes
Eg , 1.75 full turn's, 2 full turn's etc
And then turn the mixture screw back out to where it was set at.
Let me know how many turn's out it run's best at, my guess is about 1.75 - 2 full turn's
Take the bike out for a little ride to check that there is no hesitation or stumble off the throttle, it still may need a little tweaking from there to get it spot on, but it'll only need adjustment's of 1/16th turn at a time .
Then once the pilot is dialed in nice you can suss out the needle jet/clip setting and or the main jet for 1/4 throttle to wot.
I just had a look at a Service Manual for a Yamaha Chappy i found.
For the wiring diagram, see page 110 here-
http://projectmopedmanual.info/Manuals/Yamaha/Yamaha LB2 Chappy service manual.pdf
The R/H indicator's have an orange w/green stripe wire, they both connect to a dark green wire behind the head light.
I can't tell by the diagram what colour the L/H indicator light's use (diagram say's Ch, blue from memory?), but they connect to the same colour single wire from the msain harness.
There are 2x black w/red stripe wires for the low oil indicator light.
The horn connect's to one of the same black w/red wire's the oil light uses, but on the other side of the horn it has a Pink (P) wire