Let's see what's the final form of an homunculus and why.
Let's reference the creature's stats, as per the pathfinder srd
As you can see, the hp line tells us it's a "(2d10)" HD monster.
We're going to add 3 more HD, making it a 5d10 HD monster. Whether you should take the mean value of the dice or roll them depends on your DM.
Now, several other things in the statblock depend on the creature's HD.
I will start from the things that are gonna influence others, instead of top-down.
First of all, every 4th level a character gains an ability score increase. Since the homunculus goes from 2HD to 5HD, he gains one. Decide where this will go.
You will probably notice he gained it based on his total HD, not on the HD he gained over its base form. This will be true for every change we're gonna make.
If you can raise any of its abilities to an even value, this will reflect on otheer values as well. Let's say it's dexterity. Armor class goes up by one, as does the reflex save.
Second, you need to re-calculate the Base Attack Bonus and the Saves, using the Construct progression table.
A construct has all bad saves (0 0 1 1 1 progression) so it goes from a +0 to a +1 base saving throw bonus.
A construct also has a good BAB (1 1 1 1 1 progression) so it goes from a +2 to a +5 BAB.
Third, every odd level you gain a feat. So you gain one at 3 and one at 5.
Fourth, as per the construct table you gain 2+Int skill points per level (since the homunculus has a Int score) and your maximum ranks increase accordingly to your new HD.
When calculating AC and attack lines remember to factor in the +2 bonuses for size and the (eventually) new Str or Dex score