For a sequence $s = (s_1, s_2, . . . , s_n)$, define
$$F(s) =\sum^{n-1}_{i=1} (-1)^{i+1}(s_i - s_{i+1})^2.$$
Consider the sequence $S =\left(2^1, 2^2, . . . , 2^{1000}\right)$. Let $R$ be the sum of all $F(m)$ for all non-empty subsequences $m$ of $S$. Find the remainder when $R$ is divided by $1000$.

Note: A subsequence is a sequence that can be obtained from another sequence by deleting some non-negative number of values without changing the order.
1. **Rewrite the total sum over all subsequences of \( S \):**
   \[
   R = \sum_{m \subseteq S} F(m) = \sum_{m \subseteq S} \sum_{i=1}^{|m|-1} (-1)^{i+1} (2^i - 2^{i+1})^2
   \]
   This can be further simplified to:
   \[
   R = \sum_{1 \leq i < j \leq 1000} (p_{i,j} - n_{i,j})(2^i - 2^j)^2
   \]
   where \( p_{i,j} \) and \( n_{i,j} \) represent the number of positive and negative occurrences, respectively, of the element pair \( (2^i, 2^j) \) when they are adjacent in a subsequence.

2. **Claim:** \( p_{i,j} - n_{i,j} = 0 \) for all \( i \neq 1 \).

   **Proof:**
   For any given \( (2^i, 2^j) \) as an adjacent pair of elements in some subsequence \( m \), the sign of their difference is determined by the index of \( 2^i \), which we call \( k \leq i \). We add one to \( p_{i,j} \) if \( k \) is odd. Otherwise, we add to \( n_{i,j} \). Since \( k \) is the index of the first element in the pair, there are \( k-1 \) elements before it with indices in \( \{1, 2, \dots, i-1\} \). From this, there are \( 2^{i-1} \) combinations of elements that can be included in any given subsequence. Thus,
   \[
   p_{i,j} = \binom{i-1}{0} + \binom{i-1}{2} + \cdots
   \]
   and
   \[
   n_{i,j} = \binom{i-1}{1} + \binom{i-1}{3} + \cdots.
   \]
   Consider the polynomial \( P(x) = (x-1)^{i-1} \) with coefficients \( a_1, a_2, \dots, a_{i-1} \). It holds that
   \[
   p_{i,j} - n_{i,j} = \sum_{l=1}^{i-1} a_l = P(1) = 0
   \]
   for all \( i \geq 2 \). Otherwise, when \( i = 1 \), the above equality does not hold. 

3. When \( i = 1 \), \( n_{i,j} = 0 \) since there are no elements before the first. Also, \( p_{1,j} \) is simply the number of subsequences consisting of the last \( 1000-j \) terms, which is \( 2^{1000-j} \). Now, we simplify \( R \) to:
   \[
   R = \sum_{1 \leq i < j \leq 1000} (p_{i,j} - n_{i,j})(2^i - 2^j)^2 = \sum_{j=2}^{1000} (p_{1,j} - n_{1,j})(2 - 2^j)^2 = \sum_{j=2}^{1000} 2^{1000-j}(2 - 2^j)^2
   \]

4. **Simplify the expression:**
   \[
   R = \sum_{j=2}^{1000} 2^{1000-j}(2^j - 2^{j+1} + 4) = \sum_{j=2}^{1000} 2^{1000-j}(2^{2j} - 2^{j+2} + 4)
   \]
   \[
   R = 2^{1000} \sum_{j=2}^{1000} (2^j - 4 + 2^{2-j})
   \]
   \[
   R = 2^{1000} \left( \sum_{j=2}^{1000} 2^j - 4 \cdot 999 + \sum_{j=2}^{1000} 2^{2-j} \right)
   \]

5. **Evaluate the sums:**
   \[
   \sum_{j=2}^{1000} 2^j = 2^2 + 2^3 + \cdots + 2^{1000} = 2^3 (1 + 2 + \cdots + 2^{998}) = 2^3 (2^{999} - 1) = 2^{1001} - 2^3
   \]
   \[
   \sum_{j=2}^{1000} 2^{2-j} = 2^0 + 2^{-1} + \cdots + 2^{-998} \approx 1
   \]
   \[
   R = 2^{1000} (2^{1001} - 2^3 - 4 \cdot 999 + 1)
   \]

6. **Simplify modulo 1000:**
   \[
   R \equiv 2^{1000} (2^{1001} - 8 - 3996 + 1) \pmod{1000}
   \]
   \[
   R \equiv 2^{1000} (2^{1001} - 4003) \pmod{1000}
   \]
   Using Euler's Totient Theorem, \( 2^{100} \equiv 1 \pmod{125} \), so:
   \[
   2^{1000} \equiv 1 \pmod{125}
   \]
   \[
   2^{1000} \equiv 0 \pmod{8}
   \]
   By the Chinese Remainder Theorem:
   \[
   R \equiv 0 \pmod{125}
   \]
   \[
   R \equiv 4 \pmod{8}
   \]
   Combining these results:
   \[
   R \equiv 500 \pmod{1000}
   \]

The final answer is \(\boxed{500}\).