Ok I just had a sorta insight but not enough to solve the problem... for me.
The ship can travel at 1000 units per 4 minutes
The ship is 456,250 units away from the planet currently (1.25 ly) and at an angle that draws a straight line through the ship, planet and star
ships is 456,750 units from the star
let's say the planet is at (0, -500). If you travel straight to this location it should take 1.25 years and the planet should be at (-500, 0).
From this there should be some equation that could get to the number, but I'm not that good with math...
The traveling time from the targeted point to the actual point is only 2 minutes, or half a day, and that's not a lot of change. Less than a 1 degree change... and a ship would know this so they'd target this location... There's just a small bit i'm missing here and it would be solved... but i dunno what it is... something to do with the Pythagorean theorem...
edit: Ok if I understand this right... The number ends up giving me 456.750273673 days vs 456.25 days. or .5 days or .5 * 4 mins with the biggest difference that will be possible... If i understand this right I just have to figure out the distance from the original position of the planet to the position that it would be at the time of arrival at that point, which is essentially the same as going to the first position then the second.
Sooo lot easier than i thought it was... assuming the same speed as earth...i just have to figure out how to adjust the values to the right numbers now that i know roughly how to get the right numbers since most planets orbit a lot slower than Earth.