Distances are only for planets of the same sector. If you want to go to another system planet there is just a fixed sector distance (regardless of where the planet would be located inside a sector). The same goes for galaxy distance.
This would be for neighbour sectors, if you want to go to a planet several sectors away you have 2 choices:
- multiply the fixed sector distance by how far the sector is.
- always use one fixed distance, as if all sectors were neighbours.
You basicly need to choose between realistic flat galaxy cordinate system (but I don't think it would work very well with the layers of galaxy/sector you described, flat planetary map would do better) or by layers system (you warp to higher levels of coordiante system which does not care about the distance but has fixed time costs).
Or shorter, you could make it the way they did it in Stars! or the one in Reunion

Alternatively, you could go for sectors linked by warp points.
Take a note that the multiple layers of galaxy view (leading to smaller units of distance) basicly rule out distance as it is, only movement cost of the higher levels counts then (distance between planets is irrelevant, becuase the cost to move on galaxy/sector level is so high that movement between planets has to be almost instant to assure playability). By using this system you remove distances from the game in exchange for clear interface. I don't recall even one game with such view system that would have relevant distances.
Maybe try to think about it from player's perspective. How long should it take for players to move from a planet to planet, from sector to sector and from galaxy to galaxy?