There is a possibilty to completely digest Keratin enzymatically with cheap technical Proteases, they are easy to get in high activities and will not outlimit your budget.
You need to add a SH-Bond reducing agent, ß-Mercaptoethanol, Thioglycolic Acid etc.
After you can extract the Keratin more easily. This "Organosolv-Keratin" is more native, so you can choose depending on if you only want to de-ink hair or really want to isolated native Keratin.
I have successfully extracted melanin from mouse hair using a simple assay. I then went on to measure the absorbance at 500 nm, which serves as an indicator of the total eumelanin and pheomelanin.
The method is from this article:
"Advanced Chemical Methods in Melanin Determination" (Wakamatsu et al, 2002)
Note that this article states that this method has been successfully used to dissolve mouse hair, sheep wool, and human hair samples.
This is how I performed the assay using shaved mouse hair:
Dorsal hairs of mice at P50 or P100 were shaved and 1 mg was dissolved overnight in 1 mL of hot (65°C) Soluene-350 (PerkinElmer) and 10% water. Triplicate 150 μL aliquots for each mouse hair sample were analyzed for absorbance at 492 nm as previously described to generate an average absorbance value.