I almost disregard the "H" tools till after the seat stays are attached. Sure I bend the drops to be roughly parallel but as Doug said these tools do nothing to tell you about a wheel's alignment, just whether the drops are parallel to each other.
Looking at the second photo with a wheel installed I see very little (hard to even say with this view) of chain stay length misalignment. I do see quite a bit of uneven "height" of the drops. So is there were seat stays attached the L:H SS would be shorter then the RH one is. I would simply bend the CSs to achieve the correct SS length and their evenness, as confirmed with a good wheel installed prior to attaching the SSs.
What type of tubing is this? Have you tried any aligning efforts yet? I find about every CS assembly I have done requires some amount of tweaking to improve alignment before the SSs are attached.
Last thing is if you decide that you have to remove and toss out the CSs and drops I would first take this as a learning moment and find out what it takes to end up with a well aligned situation. Bending to line up, filing slots to seat the axle so the wheel is on plane. Andy