Paul, using the solid couplers appears to be a better idea, especially if they are a precision fit. To me, if the fit is snug, the alignment of the carbs would be a bit more precise and would allow that final tweaking of the fit. That said, I am using the spring clips and have had to realign my carbs twice to try and get the shaft to be truly parallel. I am only able to eyeball them so I know they are not truly perfect, hence the possibility of wear inside the carbs where the shaft ride. The downside to the Goodparts triple intake is the fact that the individual components never are in perfect alignment. I had my head flowed to match the intakes, and they were way off (the intakes, not the head). I have it as good as it gets, which is not really that good. I wish that the triple intake were a solid unit with precision-bored carb holes, or holes that could be aligned to the three carbs.
On the throttle linkage, no matter how new or good your stock-style modified linkage is, you will never get 100% throttle response. You will find that a cable will allow you to get very rapid and complete throttle action, compared to a complicated mechanical apparatus. Most modern fuel systems use cables for that very reason.