Separation of closely-sized isoforms
6kDa are usually enough to seperate two proteins in my experience. Try the other way, use a 7 or even 8% gel. They run longer but have a higher separation capacity. If you look at this figure from the LabFaQ, you see that you can use a higher percentage gel:



The other thing are the antibodies: Where are your isoforms different? 6kDa are 55 to 60 amino acids more for the long form, so there should be enough possibilities to make specific antibodies.