Thanks for all the replies. First, some details regarding the historical situation of Midway defences in 1941-1942.
http://www.historynet.com/midway-islands-undaunted-defenders-may-96-world-war-ii-feature.htm
https://www.ibiblio.org/hyperwar/USMC/Midway/USMC-M-Midway-3.html
So it can be seen that a significant amount of reinforcements, especially aircraft, hurriedly arrived after May 20th in the space of a week or so, when Nimitz had solid evidence that Midway was the next IJN objective. Now Nimitz visited Midway on May 2, but as far as i can read nothing was sent until after Midway was confirmed as the next target. It appears there's some lore that postulated Nimitz knew Midway will be next even before the Coral Sea battle (hence the visit) but recent historians like J. Lundstrom refute that. I think the timeline of reinforcements looks to confirm it.
Now as Carl points out, since Midway's defence will likely be weaker than in OTL if one is to assume most if not all the reinforcements that arrived in the last week of May actually do not arrive imo assuming that even against a weaker Midway defence the IJN amphibious assault will fail is rather far fetched. It has been done to death before, especially IJN landing doctrine and fire support, and i of course do not agree with what is promoted as "consensus", but regardless of that a weaker Midway defence of course increases by that much the probability of IJN success.
There is though ambiguity even today about the real numbers of troops on Midway and the opposing numbers of japanese troops. A figure of 3500-3600 US troops is frequently quoted, though in BSCA the figure is actually stated as "over 2000" (you would think that there would be record somewhere of the exact number of US troops on the island in early June surely). As for the japanese the lowest number is quoted by SS at 2500, but frequently the japanese number is stated as 5000 troops, and as high as 5800. SS postulates that difference is made by "labour batalions", now whether there is an error and actually the labourers were EXTRA to the 5000 or so troops i'm not sure. Of course, i have tried to find info of how many men Ichiki and Ota had in their respective contingents. This source appears to say that the labour batalion (only one?) was in addition to the IJN and SNLF detachments (numbering in total) aprox 5000 troops.
http://www.ibiblio.org/hyperwar/Japan/Monos/pdfs/JM-93_MidwayOperations,May-June42/JM-93.htm
Another thing i looked over was the number of transports used in MO operation (11) embarking approx 5000 troops (there were again some labour units planned to be landed at Port Moresby, and it also appears they were extra to the over 5000 IJN/IJA troops), compared to Midway (16?). It would be very puzzling to have more transports carrying just half the number of troops compared to MO.
So, IF the number of US troops is lower at 2000 something with fewer guns and less preparations (maybe even no tanks), and IF the number of japanese troops is over 5000, then actually the requirement of 3 to 1 superiority for the attacker is almost met.
As for Kido Butai, if there is no carrier battle, considering the weaker Midway defences they probably have in total about 20 aircraft lost or written off over a couple of days of attacks. If Yorktown is not at Pearl and/or it and Saratoga are not sent to challenge the invasion force then Nagumo, having suffered only light losses, will probably be sailing for FS at the end of July, likely joined by Zuikaku - and at that time probably the US carriers are preparing to assault Midway, or they are still split, 2 or 3 in the South Pacific, 1 or 2 on the West Coast (not sure if they would keep any at Pearl given the likely nuisance raids from Midway), or of course some other possibility.
Come to think of it, getting back a bit earlier, probably operation K succeeds in this TL, what they will find at Pearl, just Yorktown recently returned from the South, or maybe no carrier/s at all if Yorktown is sent straight to the West Coast.