Okay here is my finalsun overlook on it...
-concerning your blue line bug, as i haven't looked at it ingame i'm not sure what it is doing there but obviously after opening the map up in finalsun the red line is lower than the blue one.. to fix this go to Edit-> Map and then look into the visible area. it currently reads 2, 2, 66, 74. It needs to be 2, 4, 66, 72.
How you managed to get that to happen is beyond me except maybe toying around with the wrong parameter number. I think to fix the bottom one on the cliff you probably changed the 2nd number to a 2 to raise it up, however, the 1st 2 numbers in that set are the Left side and Top placement ones and those are independent. However the last 2 numbers are dependent and decide your length out to the right and the length down in which your visible area spans.
Meaning if you change one of the 1st 2 numbers then you will also be moving the right and/or bottom line too. So to move just the right side or bottom line some you need to edit the last 2 numbers only.
I hope you understood that.
-Cliffs. It seems you're getting there...but you still need work with them. Attached below is an example picture from one specific spot.

-Blockiness still seems to exist on your hill slopes here and there. It also is really noticeable in your LAT and the water.
-Water, the water is actually fine for the most part. No Shore errors. I personally have become a fan of non-cut up water tiles, which you have in your map but they are harder to notice than normal LAT tiles that are cut in half and many many a maps have it in them. The main thing in the water that concerns me is the swampy lat. the pieces that have the blue bright stuff in them need to be completely surrounded by the first 1x1 tile in the list as otherwise it will not auto-form itself and you'll have a straight edge of swampy LAT against water which looks bad.
-As for lighting, I haven't played it ingame obviously, and your screenshots are of finalsun. However i checked the global lighting and it's your basic lighting still. So all the lighting additions to this map are from the lightposts, which the reason your blue probably doesn't look like the blue lighting i have on my blue tib in Hells Crevice is due to the effect of global lighting has over it and the negative colored light post i have there. On the map it's a purple light post next to the invisible blue one...in the map file though it's values are changed so that it takes away red and green lighting, thus leaving the blue lighting to dominate that area.
As you probably would guess global lighting is slapped on the map when you put it in. Thus if your global lighting is a redish color and you throw in some blue light posts the area the blue light posts are in will look purple ingame unless you put up negative red light posts around the same general area as the blue ones.
-concerning the VHM. It looks alright...but you need to keep in mind that the center of a VHM is actually 1 cell down and thus if you place it on flat ground you'll find that in game that, the center spot will magicly be one height level down upon destroying the VHM. This can be avoided by making sure you start on an area where the height level is 1 and not 0. Then placing the VHM, then using the Lower Ground (slope logic) button click on the center of the VHM. This will properly make the VHM spot, although on occasions it will not be accurate for some reason and thus you'll have to retry. To spot it if it doesn't work simply place the veins around the edge of the VHM and if they overlap with the VHM something is wrong.
You are showing signs of improvement from your first map on here and that's good. Just keep working with them and you'll get better as you create more.