Could be several things that would be making it act that way.
1st is what you already mentioned, Make sure the rod is long enough to actuate the master fully. Custom installations usually need you to make some custom parts. That may be a hardened rod , so don't just throw a piece of mild steel rod in there if needs a hardened one.
2nd does the master need a kit in it? Even if its new off the shelf, it could be bad or put together wrong. Fluid doesn't compress, so if you are getting full travel on a good master cylinder it has to come out of the lines at the wheel cylinders or leaking some place.
3rd would be a leak, but you probably checked that all ready.
4th: wheel cyl cups in backwards?
I have seen all of these.
Just start from the master and go through all the steps to the wheels and don't skip anything. Most generally everything will start working right. Make sure to keep that master full while bleeding.
