Please clarify: is your problem a) judging which intersections to consider territory or b) counting the intersections that are already known to be territory?

First count Black's territory. Remember the number. Then count White's territory. Form the difference and include the komi (for White!).

To count a player's territory, proceed region by region. Count each region exactly once. Although you count region by region, you update and increment only one number per player. When you have determined a number of the first region, start with it when counting the second region etc. Thereby you do not need to recall one number per region. It suffices to recall one number per player, for all his regions together. And the prisoner stones of opposing colour; after the last region, add that number of prisoners.

To count a region, first count the intersections occupied by dead opposing stones, then count the empty intersections. For each intersections occupied by a dead opposing stone, add 2 to the total number for the player. For each empty intersection, add 1. When counting a region's intersections occupied by dead opposing stones, proceed line by line of the board from left to right. When counting a region's empty intersections, proceed line by line of the board from left to right. Do not accidentally miss a line or scan a line twice.

Whatever needs to be done, also change a number exactly by the summond. Never forget the hundreds or the tens of your currently updated number.

Practice this procedure, until you do it correctly without failure. Only afterwards, consider using simplifications.

The procedure is slow, but should be safe.

It's not that hard, once the game is almost over.

This is the position (I just realized that I only got 0.5 komi since I played against someone weaker, on the board I have 43 points less). Just now I tried recounting it 3 times, but I counted it to be very close each time.

When counting a region's empty intersections, proceed line by line of the board from left to right. Do not accidentally miss a line or scan a line twice.

How do you learn to count a game?
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I just lost a game by more than 40 points, and I thought I was winning. I am 4d KGS

it is hard to believe that you can reach a solid 4d on KGS without being able to count.

As you don't give your KGS handle is it hard to check, but it is hard to believe that you can reach a solid 4d on KGS without being able to count. Was it gained through a large number of blitz games won on time? If you really do have a solid 4d there then it is a sad reflection on the KGS rating system.

I wish there were counting problem books. Some of the positional judgement books have some problems, but it would be nice to have a tsumego type book with the board position on one page and the answer with the number and squares that were counted on the next. I know counting positions is sort of voodoo, but I think there should be enough positions that are figured out at the amateur level to fill a book or two.

Every game you play or watch is a counting problem surely?