If not in actuality, were there at least formal plans for the two nations' armed forces to link up and execute an allied strategy against their enemies? If not, why do we refer to these nations as having had an alliance at all (beyond the simple formality of the documents they signed)? It often seems, when I study the history of the war, that the two nations were "doing their own thing" completely independent of each other.
Japanese-German cooperation was very rare, and as such, very few records actually exist.
At first, the conquest of Poland allowed direct material and science exchanges through the trans-Siberian railway, but these were very few and would have resulted in little, if anything, due to shortages on both sides.
After the closing of the railway due to Operation Barbarossa (and the clear failure of the Germans to open up trade links through the Suez in Africa), the only contact the Japanese and Germans could ascertain was through submarines. Numerous designs, especially torpedoes and submarine detection systems like Metox, were exchanged in places like Lorient in France or the Indian Ocean. The Japanese sent the most submarines to Europe, however close to the end of the war it was Germany sending U-Boats to Japan. The last such mission (U-234) never finished as it surrendered due to the closing of hostilities in Europe. It was carrying uranium oxide and plans on how to create heavy water, vital for the production of nuclear weaponry.
In terms of combat assistance, there was very little and mostly relegated to the naval side of things. German auxiliary ships Micahel and Thor went around the Cape of Good Hope, as did a few German U-Boats. The U-Boats were relegated to the Indian Ocean along with a few Italian subs, but the cruisers fought throughout the Pacific and were supplied from Japanese ports. All prizes were given to the Japanese due to inability to send them to Europe.
Put simply, it was not in any way an alliance that could hold it's water. Sheer reality stomped on any hope that the Germans and Japanese had for a practical alliance, and the scientific and material exchanges between them were to few to add anything to either's war effort. No long-term planning or real coordination of military operations of both powers ever happened.
As you put it, it was a de-facto NAP. They did draw up plans for post-war spheres of influence, but these were never concrete and both states considered the other the enemy of the future. Think of the Allies and the USSR, but with lend lease only occurring once every 3 months.