have to say the SR71 designed by a lean team and fairly small budget in 1960s is a true miracle for the tools and knowledge base of that era. its peers were the sabrejet and F-104 types. the combined turbojet + annular ramjet at higher speed....very non-linear A++ thinking level, the materials used, the space suits for the pilots, dealing with the leaking fuel, thermal management. probably these all were all first timer problems encountered.
Fuel leak was calculated down to the number of drips and they wrote acceptable limits into the SOP's. Kelly was once asked by a young engineer on what could be done to stop the drips, and he put a cash reward for anyone in the company that could solve the issue because he did not think it to be relevant operationally. The prize was never claimed throughout the life of the aircraft.
The biggest issue was the Titanium and machining it, and they had multiple design iterations. First they tried to run this thing on Liquid Hydrogen, and that did not go well for them
before it was dropped. The A-12 was the 12th iteration so they tried quite a bit. I may not remember exactly but i read somewhere that there were as many patents filed for the manufacturing process as were for the design features and components.
When Kelly originally designed the SR-71, his roadmap envisioned speeds all the way up to Mach 4 as the design matured as he thought that this would be required to keep the thing relevant over its entire 30+ year life. The maximum speed claimed is mach 3.4 by the lockheed test pilot but that was heat limited. Of course with the SR, it was as much about top speed as it was about sustaining Mach 3.2 (thats the speed where the sensors worked their best) for prolonged periods at altitude. Who knows what the skunks did that is not known to us as till this many aspects of the design program (In addition to the operational, and development of the oxcart and SR programs) are not openly discussed (and may even be classified). Interestingly when they were testing the RATTLRS in one of their briefings the lockheed employee said that we have testing data for this concept till mach 4 before he shut up and changed topic. There used to be a video of that somewhere on the internet, i'll try to find it.