I'd highly recommend using a cold saw to cut the pieces to length. The squareness that can be achieved with a cold saw may be good enough to cut without a subsequent facing cut on the ends. Just a thought.
The first step I would take would be to machine the rounded mill edge off the edge of the angle legs. Even extruded angle may not have the thin edge of the legs truly flat and parallel to the outside of the opposing leg of the angle.
Place the angle in the vise with one flat side down on the base and one leg of the angle sticking up, and resting against the fixed jaw of the vise. Use a piece of rectangular stock or a 'rough use' 1-2-3 block spacer between the movable jaw and the upward leg of the angle. This spacer does the clamping up near the top of the vise jaw. Then, you should be able to machine the mill edge of the angle without a lot of squealing.
Facing the ends of a longer piece in the vise might work better if done as a seperate operation with the part laying in inverted V, with the apex of the angle up, and each leg nested down between the lower corners of the vise jaws and their base. However, this could require enough vise clamping pressure to spring the part (if it is flimsy). If you happened to have a set of step jaws for your vise, turn them with the step down, with the intent to get the edge of the step to overhang the 45° angles of the part laying with the back of the V facing upwards. This would prevent the endmill from 'augering' the part up when facing across the ends, and yet you would not have to tighten the vise up with excessive force.
For short pieces of angle, balance the load in the vise with identical pieces at each end of the vise jaws, or suitable spacer to accomplish the same thing. Use a few narrow strips of paper between the part and the vise, so you can detect where the clamping effect is taking place. You want two tight spots, not one, along each jaw of the vise.
This style of laying the angle with the apex up in the center in the vise, should shorten up the length of endmill by required to reach to full depth for the facing....maybe Use a large heavy endmill in as stubby of a holder as you can get hold of.
After the edges have been squared, then you should be able to use that machined edge as a good clamping surface in the vise. It would be worthwhile to machine a deep set of vise jaws that can accept 4" depth of stock. However, a deep set of jaws used in a standard 1.75" mill vise might suffer from a 'tilt gap' when the part is at the very top of the jaws. The part could destabilize or be impossible to 'hammer down'. Do your best to keep the jaws from tilting with a custom fit spacer laying in the bottom of the vise, and forcing the downward leg of the angle against the fixed jaw. One of those adjustable parallels would be a good solution for this custom spacer.
You need to balance the clamping effect from top to bottom of the extra deep vise jaws. Use of pieces of paper between top and bottom can help you detect if the clamping effect is shared equally. If you cannot pull the paper strips out, then it should be evenly clamped.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)