You are correct that the cylinder needs to be limited to expanding a single, on axis stripe. However, assuming these beams have already been PBS combined and the expansion will widen the stripes then you can very effectively expand the 2 vertical stripes (4 beams) into a square that will fit a 6 mm aperture scanner. The problem with the prism is that the horizontal location of the beams COMBINED with horizontal expansion will quickly produce a wide rectangular beam at even modest expansion and that beam will be only 3mm high.Here's a question I think very relevant to the topic title: isn't one fundamental difference between cylindrical lenses and prism pairs for doing knife edging the fact that with prisms you can stack the "tall" beams horizontally and have them expand equally while with cylindricals since the beam has to be in the exact center of the lens you have to expand these tall beams stacked vertically? With the latter I don't see how you could knife edge any of the multimode 500mW+ diodes without hitting the scanner mirror size limit with more than two diodes.
Firstly, never use the TEC's to cool the heat sink. This should be limited to high heat capacity extraction with fine fins and a powerful fan or better, water cooling like the CPU water cooling modules marketed by computer companies. The TEC's are so inefficient that the heat they add to the small heat from the diode is what limits is your ability to remove all this combined heat. This heat extraction needs to occur with as little warming as possible to the side of the TEC where the heat is being extracted. This surface can become hot and the differential may be large, but the diode sees little net drop from ambient.I got another question for you Planters....how do you get your TEC pelters to drop below zero degrees?
Condensation of humidity from the surrounding air, on the cold surfaces, produces a lot of energy and this needs to be prevented in order to reach lower temperatures. Cover the TEC stack with an air tight box.