How can I find if a raycast has passed through two points?

You could create a mesh collider (plane) on a run between A and B with some height (must be relatively high depending on flatness of your level).

1. Raycast C-D

2. On Found D create mesh collider

3. Raycast Again same direction

4. If hit your mesh set some flag or continue with your code.

Just a theory never tried it.

You're probably best off looking for a 3D line to line collision test off Google and porting it to Unity (unless you need a 2D test, which is faster to calculate).

See if this works for you (ported from StackOverflow)

 using UnityEngine;
 using System.Collections;
 
 public class Test : MonoBehaviour {
 
     
     bool LineLineIntersection3D(
         Vector3 LineA_Pt1,
         Vector3 LineA_Pt2,
         Vector3 LineB_Pt1,
         Vector3 LineB_Pt2, out Vector3 IntersectionPt)
     {
         Vector3 da = LineA_Pt2 - LineA_Pt1; 
         Vector3 db = LineB_Pt2 - LineB_Pt1;
         Vector3 dc = LineB_Pt1 - LineA_Pt1;
         
         if (Mathf.Abs( Vector3.Dot(dc, Vector3.Cross(da,db) ) ) > Mathf.Epsilon ) // lines are not coplanar
         {
             IntersectionPt = Vector3.zero;
             return false;
         }
         
         float s = Vector3.Dot( Vector3.Cross(dc,db),Vector3.Cross(da,db)) / Vector3.Cross(da,db).sqrMagnitude;
         if (s >= 0.0f && s <= 1.0f)
         {
             IntersectionPt = LineA_Pt1 + da * s;
             return true;
         }
         IntersectionPt = Vector3.zero;
         return false;
     }
 
     // USAGE EXAMPLE
     void Awake()
     {
         Vector3 v3Intersection;
         if( LineLineIntersection3D( 
                     new Vector3( -1.0f, 0.0f, 0.0f ),      // Point A
                 new Vector3( 5.0f, 0.0f, 0.0f ),    // Point B
 
                  new Vector3( -1.0f, 0.0f, 3.0f ),    // Point C
                    new Vector3( 5.0f, 0.0f, -7.0f ),     // Point D
                    out v3Intersection ) )
         {
             Debug.Log( "Intersection at " + v3Intersection.ToString( "F4" ) );
         }
     }
 }