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Ah well I've found the modifiers and it's meh.

Now I've added Supply limit bonuses to Roads, Harbours and Forts as they were supposed to have in the first place.
 
Please could you post what you did, I'd like to add them too. Thanks.

It's fairly simple to mod these games, just don't forget to backup any files that you tamper with.

1.Go to Rome's installation directory and locate the buildings.txt file, which in my case is in Program Files\Europa Universalis Rome\Common\Buildings.txt
2. Find these modifiers below, you can just scroll or search for "roads"
roads = {
cost = 50
time = 365
trade_transit_capacity = 1.0
movement_cost = -0.5
}

and then add this without quotes: "supply_limit = 0.05" beneath movement_cost = -0.5 so you get this:
roads = {
cost = 50
time = 365
trade_transit_capacity = 1.0
movement_cost = -0.5
supply_limit = 0.05
}

If you want this building to increase supply limit even more just change to 0.1 instead of 0.05, or just experiment with numbers until you are satisfied. You can repeat this for all other buildings, just find them in buildings.txt