You can never completely work around the stock injectors using an S-AFC unless you use race gas or alky. You need something that allows you to pull out significant amounts of fuel (mainly in the peak torque/mid-range), so that you can get the AFRs AND timing you need in order to make both great TQ and HP. With stock injectors on pump gas, you can make good HP, but you can't make good TQ. I've been through all that and been very successful, but in the end, you just have to decide on a flash or injectors. Frankly, I am not fond of having to mess with the stock injectors when they are plenty big for the stock turbo all the way up to 400whp, but there are many people (mainly in SoCal) who prefer that route almost to the point of stubbornness.
What I did after I finally gave in and got a flash was use the SAFC to fine-tune on a daily basis while also using it to tune for race gas at the track. This is a great method and works wonderfully, because you get the best of both worlds. You get the extra flash features (2-step launch control, raised rev limiter, removed fuel cut, idle speed control, and topspeed limiter removal), the awesome peak torque with broader torque curve, and the fine-tuning ability for changing conditions and octane.
Yes, your timing fluctuations indicate knock, and you are rich from 4300-5400 then rich as hell after 5400. Wait until you have the wideband before you lean it out, though. I'm not fond of the Uego, because it doesn't read below 11.0:1, which is kind of important, especially for you right now, haha. If they have changed it, then disregard...