Yeah, that's quite a gash.
Although, your finger length doesn't look like a problem to me.
One question: You said your right index finger is the one which was injured. Why is the photo showing your left index finger?
My index finger is considerably shorter than what you show in your photo...and I never had any injury:
To compensate for the shortness, I have to arch my middle and ring fingers so all four fingers meet together on the string "inline." I don't necessarily adjust my hand angle...just the finger arching:
I'm sure the tone variance between your index & middle finger is frustrating. Is it the skin, or just a lack of finger pad? I don't want to be indelicate, but is it because your finger has less meat on it or is it just callous skin?
You may want to check into getting fitted for a durable prosthesis. With today's technology, I'm sure you can find something good.
You could also try to isolate and dial out the offending frequencies with a good EQ. You can play a note with your index finger, then your middle finger and compare both in a spectrum analyzer...isolate the frequency variance and try to dial it out.