If you do a quick flush with alcohol, you should use less than a gallon figuring 50' hose. Then go ahead with the ammonia and let that set in the pump and lines for awhile.
For the cost of a 50' hose, I'd suggest keeping one hose entirely set aside for doing shellac based sealers. I do that with those and any oil-based sealers have there own hose set-up also. In the long run it is a money saver for an initial investment of around $100 or so.
Also, when you do your final flush, take the manifold filter out after, and let it soak in the appropriate cleaner.