The Vallejo 70,898 Dark Sea Blue Model Color FS-35042 and the 71.300 Glossy Sea Blue Model Air FS-15042 are the same indeed. The difference is that the fist one is the matt paint while the second is the gloss one. Therefore the first colour is also known as the Non specular Sea Blue. The Tamiya XF-17 Sea Blue is the FS34058 and is considered as a colour of a little too greenish tone by many of guys assembling models. So I would stay with the Vallejo 1.300 Glossy Sea Blue Model Air FS-15042.It is a good representation of the ANA 623 paint.
The Vallejo 70,838 Emerald isn't of a good tone. I would say the Vallejo 70.891 Green Medium is fine and I would follow that one. The Tamiya X-28 Park Green also look good.
As far as the final finish of the plane is concerned I would say it should be gloss. But the semi-gloss sounds good too.