Note for optimization: So, basically a shortest Hamiltonian path with 2 twists (condition 1 & 2). Considering shortest HP can be solved with a Travelling Salesman algorithm (with a dummy city with zero distance from all others), for a better optimised solution you could try manipulating your distance matrix according to condition 1 before feeding it to a TSP algorithm.
More on how to use TSP for this shortest HP here.
Brute force approach
I'm gonna call your points [A, B, ...C] for readability. Let's represent our points like this:
+---+---+---+
| | X | Y |
+---+---+---+
| A | 0 | 0 |
| B | 4 | 3 |
| C | 0 | 3 |
+---+---+---+
Then create a distance matrix with the Pythagorean theorem:
+---+------+------+------+
| | A | B | C |
+---+------+------+------+
| A | 0.00 | 5.00 | 3.00 |
| B | 5.00 | 0.00 | 4.00 |
| C | 3.00 | 4.00 | 0.00 |
+---+------+------+------+
My understanding of your first condition (fix threshold) is that any distance lower than a certain value is considered zero. Apply that condition to the distance matrix (let's say it's 3.50 in our case).
+---+------+------+------+
| | A | B | C |
+---+------+------+------+
| A | 0.00 | 5.00 | 0.00 |
| B | 5.00 | 0.00 | 4.00 |
| C | 0.00 | 4.00 | 0.00 |
+---+------+------+------+
Now, if we keep to our brute force approach, we must fund all possible permutations of routes. In our case, it's going to be simply
+------+-----------+--------------+
| Path | Distances | Total Length |
+------+-----------+--------------+
| ABC | 5+4 | 9 |
| ACB | 0+4 | 4 |
| BAC | 5+0 | 5 |
| BCA | 4+0 | 4 |
| CAB | 0+5 | 5 |
| CBA | 4+5 | 9 |
+------+-----------+--------------+
Remove routes that are the same but reverse.
+------+-----------+--------------+
| Path | Distances | Total Length |
+------+-----------+--------------+
| ABC | 5+4 | 9 |
| ACB | 0+4 | 4 |
| BAC | 5+0 | 5 |
+------+-----------+--------------+
Take the shortest by total length and that is your solution.
2nd condition - distance covered on X is preferable to distance covered on Y
As far as I understood, this condition only activates if there is a tie in Total Length. In that case, create a distance matrix by using the absolute value of the difference in the points' X coordinates:
+---+------+------+------+
| | A | B | C |
+---+------+------+------+
| A | 0.00 | 4.00 | 0.00 |
| B | 4.00 | 0.00 | 4.00 |
| C | 0.00 | 4.00 | 0.00 |
+---+------+------+------+
Sum up the distances according to your tied routes and use the min of that to decide which one should be preferred.