As a result of severe boredom, I ran through the plans again. I actually quite like the switched sides on Hanover St, lets you use the road downhill in both directions before joining the cycle lane uphill. Some oddities I noticed/rambling:
Seems odd to just ban the left turn from George IV to Chambers St. I would imagine a separate cycle phase would still be needed if right turns are permitted.
Yellow box at Candlemaker Row, potentially unnecessary? Due to the short distance between both sets of lights, further reduced by the yellow box, I can imagine the remaining drivers blocking the cycle crossover at Forrest Road when the lights are red at George IV/Chambers St. Although syncing the lights well here would mostly fix this.
9.72m long ASL on Market St. A world record?
The cycle lane doesn't appear to be raised at mini-zebras which seems unusual.
The pavement is actually reduced by quite a bit outside the National Museum. Could the on-road cycle lane here be removed to add some extra pavement width?
The junction at Teviot Place is just odd. If you're coming from the uni and want to head to MMW, there's give ways with the actual stop line earlier on Forrest Road. Like @bacam mentions, the south side seems like it would be a simpler solution. Plus a wide 1.5/2.5m buffer wouldn't be needed since there's no bus stop/loading.
Market Street: I believe there was some controversy over the taxi rank here. Why not swap the taxi rank with the large loading bay to bring it closer to the station?