Re: High e string intonation very low
The neck needs to be in a concave position when strung up to pitch. You can check this by fretting the low E string at the 1st fret, then at the last fret. You should then be able to push the string down towards the 8th fret and have enough movement where you can sense the string is above the fret. We are talking about .5mm or so. This can vary, but at least .5mm is a good starting point. The truss rod adjustments should not be used to alter string height. The change to the string height is a byproduct of truss rod adjustments. I hope this makes sense.
Once the truss rod is setup, make sure the guitar is strung to pitch. Then confirm the bridge is level with the body of the guitar. I have never tuned an "Edge" Trem, but have done the lo-pro and Edge II. The Edge II just needs the top of the base plate to be level with the guitar. The lo-pro has an angled top plate. To help with alignment there are tabs on the side of the base plate that help with alignment. I have no idea on the "edge", which is what I think is on your guitar. Use the Trem springs on the back to make adjustments and get the bridge level. After every adjustment, you have to re-tune the guitar and start over.
Once the truss rod is setup correctly and the bridge is level you can then deal with the action. Measure the action and make adjustments at the bridge posts.