A subject on which entire books have been written, some of the basic source information:
US 6th Army report on the Japanese plans for the defense of Kyushu can be found at the CARL site, specifically here:
The summary of this report, in part states:
“By the end of July 1945, sufficient information was available for the G-2 to make a preliminary estimate of the enemy strength in KYUSHU. In the Sixth Army G-2 estimate for the OLYMPIC operation, dated 1 August 1945, it was estimated that 421,000 Japanese troops were on KYUSHU, comprising nine divisions (or division-equivalents), plus a large number of base and service troops, and naval personnel. Subsequent information, obtained prior to the end of the war, including new identifications and estimated reinforcements, raised the estimated total to 680.000, including fourteen divisions (or equivalents). This figure was reached just prior to the end of the war.
“Information secured since the occupation of JAPAN reveals that the overall total strength on KYUSHU of Japanese units of all services and types as of the final day of hostilities totaled approximately 735,000, including fourteen divisions and seven independent mixed brigades. However, this total includes units on the islands off-lying KYUSHU, which were not included in the Sixth Army estimate of the situation. Strength on these islands totaled approximately 25,000 and included three independent mixed brigades. Thus, the Sixth Army, 1 August, estimate was based on information procured in May, June, and July, and full allowance was made for large scale reinforcement, while the projected (but never published) revised estimate with complete information was 96% accurate. The discrepancy in 1 August estimate was largely caused by the underestimation of naval ground troops, whose number was greatly swelled by recruits undergoing boot training and by crews from ships which had been immobilized by allied attacks, and from troop units in transit.
“The Japanese expected our invasion of the home islands, they expected it to be made during or after October 1945, they expected it to be made in southern KYUSHU, and that our landings would be made on the beaches of MYAZAKI, ARIAKE-WAN and SATSUMA PENINSULA. Their avail¬ able combat forces had been deployed according to these expectations, with reserves being strengthened when hostilities ceased.
“Allied convoys approaching KYUSHU would have received mass suicide attacks by every available plane in the KYUSHU area. Transports would have been the main targets of these attacks, and the Japanese expected to destroy 10% in this manner. Offshore, the landing forces would have been hit by large numbers of small suicide craft and submarines, and the Japanese expected to destroy 60 transports by these means.
“Once a landing or landings were made, a decisive stand would have been initiated. Placing much stress on artillery, and having three tank brigades, one independent tank company, one independent regiment, and four self-propelled gun battalions to support division troops in their operations, the Japanese forces planned to make a final stand near the beaches and units were instructed to remain in place until an¬nihilated. Heavy counter-offensives in the beach areas were planned and little preparation was made for defense in depth.”
The remaining 30 pages of the report draws from detailed reports provided by the Japanese 2d Demobilization Headquarters, which prior to the surrender was the headquarters of the 2d General Army charged with the defense of Kyushu, and interrogations of members of that command.
I recommend the Combined Arms Research Library (CARL) digital collection as a source of information, both US and Japanese. A simple search of WW2 operational documents for the word “Kyushu” returns 163 documents.
For example. http://cgsc.contentdm.oclc.org/cdm/singleitem/collection/p4013coll8/id/4775/rec/41 presents “Documents submitted to the Supreme Commander for the Allied Forces by the Japanese mission to negotiate surrender. Manila, 19 August 1945. Full translation in two parts, part I” which amongst other items
Army air strength and organization; data on airfields in and around Japan; and naval strength, organization, and dispositions aviation facilities . . . all of which would have had some impact on a future invasion of Kyushu had it come to pass. Part II of this document, found here,
provides more information on airfield facilities and, on page 27, a map showing major troop organization in the Second General Army area of operations, including Kyushu.
One can also find amongst the CARL documents related to Kyushu: “Statements of Japanese officials on World War II (English translations)” found at http://cgsc.contentdm.oclc.org/cdm/singleitem/collection/p4013coll8/id/4761/rec/54
The abstract statement notes “Statements concerning defense preparations for southern Kyushu . . .” and, here, the very first item in the document presents the statement of a Major Tabata, Ryoichi, the former operations officer for the 57th Army addressing defense preparations for Southern Kyushu. There are other statements from IJA & IJN staff and command officers which relate to the defense of Kyushu.
The link to their collection of WW2 operational documents is here
There are also a couple of post war monographs from Japanese sources produce on by the order of the Headquarters, USAFFE addressing the subject and may be of interest.
Monograph Number 85 – “Preparations for the Counterattack Against the Enemy Invasion of the Homeland,” (71 pages) found here http://www.ibiblio.org/hyperwar/Japan/Monos/pdfs/JM-85/JM-85.pdf which discusses the Japanese estimate of US capabilities and resources and the plans for the Japanese response to an actual invasion
Monograph Number 17 which incorporates numbers 17, 18, 19, & 20 “Homeland Operations Record,” found here http://ibiblio.org/hyperwar/Japan/Monos/pdfs/JM-17-18-19-20/JM-17-18-19-20.pdf, some 278 pages, which covers some of the territory covered in Monograph 85 but also provides detailed information on major troop dispositions and headquarters and preparation for the final defense of Japan against invasion.