You appear to be missing the washer under the main jet. You need that. Combined with the main jet, that's what holds the needle jet in the carb body. Get genuine butterfly shaft seals, not the knock-offs from Mike's. They're cheaper and, of course, better. Best deal is to use the Suzuki part, same seal as the Yamaha one only cheaper .....
https://www.partzilla.com/product/suzuki/13651-51010
Don't put the plugs back over the mix screws, leave them "open" for future adjustments and tinkering. If the screw heads on the mix screws got damaged by drilling too deep when removing the original plugs, replacement assemblies are available and reasonably priced too .....
https://www.partzilla.com/product/yamaha/12R-14105-00-00