-not map expert-
I /think/ the water problem is from your terrain mask. Perhaps you colored too much blue, which will be where your water is.
To fix the portal position, go to the mapmaker, load your map, and check the "Has Portal" button. Mouse over to where you want the portal to be, and take a look at the bottom right hand corner.
Then, in the "Destination Position" type the numbers you see in the bottom right. Leave out the decimals for the first three. Order is important.
What you see: 1920.12, 1233, 1139.1, YAW: 345.15
What you type:
W: 1920
Y: 1233
Z: 1139
YAW: 345.15
Hope this helps.