It was at the extreme end of their aircraft range, especially with a Zeke (Zeke land based squadrons were use to supplement carrier based squadrons for Fleet 1 and Fleet 2) but for planes like the Nell (based in Wake and the Marshalls) with a range of 3,500 miles, doable. The Japanese scouts and bombers were able to provide the necessary air cover for the fleet as it made its way to Midway.
Well heres the breakdown, the order of battle of the shore based aircraft of the 11'th Air Fleet of the IJN at Midway.
At Wake Island, which is 1,500 miles from Midway Island.
36 A6m Zero's, range type 21 anywhere from 1,700 to 1,900 from a land base with full drop tanks. This isnt however "combat range" which is closer to 500 to 600 miles.
10 G4m "Betty" Bombers. Range about the same as the Zero. About 1,700 over all.
At Kwajalein Atoll, which is 1,806 miles from Midway.
36 Zero fighters, "Im assuming every one at Midway was the type 21".
36 B5N2 Bombers with a range of 1,237 miles.
At Aur and Wotje Atolls, both about 1,630 miles from Midway.
36 Zero's.
36 B5N2 bombers.
At Jaluit and Wotje Atolls were 36 H6K flying boats that did have a range of 4,000 miles and could have been useful but the fact is I cant find any record of any operations even around Midway and the 11'th only patrolled around there assigned bases. The exception was a plan for the H6Ks to fly to the region, after Midway was taken, to refuel from Navy ships, and to continue on to Oahu to attack there. Which of course never happened. Other then for the sea planes Midway was simply to far for the other combat aircraft to project power or to even scout. "Range" isnt "combat range".
Regarding Nagumo's orders he had more then one and it just helped conflict him and in the end defeat him. Yes Yamamato did order him to hold back 1/2 of his force for the USN CVs but everybody knew even before they got there that one land attack wasn't going to be enough. What choice did he have but to order the planes standing by to be armed for ground attack?
Changing ordinance was a very time consuming thing for the IJN because 1, it all had to be done on a lower deck "on IJN CVs all arming and fueling was done on a lower deck". And to change a 1,800 lb torpedo to a 1,700 lb bomb on a Kate needed a special cart for the ords and each CV only had 5 or 6 of these carts. Plus on the Kates you also had to change the carriage, torps and bombs had different ones. So now your in the middle of that cluster and all of a sudden USN CVs are in the area and now you have to change back to torps? on a crowded, very crowded, lower flight deck? And once you get all this done you have to inch those huge bombers onto an elevator and bring them up? See the USN gassed and loaded bombs for the entire squadron on the top deck and then <whoosh> they all took off. The IJN didnt, they did it separate flights at a time with separate airplane types.
Now for the Army to even agree to the plan they had to #1 Come along with an invasion force in ships THEY commanded and with orders that their main priority was to invade and occupy Midway Island. In fact the army only went along with the plan because of Doolittle's raid. They had wanted to invade Australia and they couldn't give a damn about USN CVs they wanted Midway and then Hawaii. Even High ranking members of the IJN General staff gave conflicting orders to Nagumo telling him Midway was the target and not the CVs. It was the same general Staff that had insisted on the stupid Aleutian offensive which took significant striking power away from the Midway Op for no good reason. They were way to far north to support the Midway operation and how can you drain resources from an enemy that didnt care if you grabbed a few meaningless Islands you couldnt possibly hold.
So it was with all these conflictions, screw ups, inter-service rivalys, conflicting orders, conflicting strategic visions, Nagumo found himself with on the faitful day.
It was just a bad plan. They trained poorly for it, they split their forces for no good reason. They underestimated the enemy and their traditionalist military methods were a real big weakness.