Did the twin-bank 539 ever make it ***onto*** the drawing board? That is, was a fully worked out, detailed, design made, or was it just back-of-an-envelope, "How about this to get a shorter and lighter engine?" brainstorming?
Anyway, more information from Kirkland's book-- sorry for the delay.
Page 95: "Alco's Schenectady plant was quickly tooled up to build the model 244 engine. Alco's McIntosh & Seymour plant in Auburn continued production of the model 539 engine. [...] Manufacture of various types of engines for marine and stationary power plant applications was continued at Auburn."
And: "Further development of the model 241 engine at Auburn was terminated. The last model 241 engine, serial #4447, was completed on August 31, 1946." (But see below-- this "241" engine was actually an Auburn-built 244!)
Page 96 has a list of the first dozen 244 engines built in Schenectady, by serial number (Schenectady engine serials beginning with 10000). Dates of completion of the engines aren't given, but as a proxy we have the delivery date of the locomotive the engine went into. The first seven are 16-cylinder engines, two of which went into Santa Fe 51 and 51A, which-- though not delivered to the Santa Fe until September-- were released for road tests on the Lehigh Valley on 27 June, 1946. (The very first, however, was "delivered" for use as a stationary test engine, and not put into a locomotive until 1949.) 12-cylinder engines start with 10007; the first three went into early RS-2 and RSC-2, with 10010 going into GM&O FA-1 727, delivered on 26 September, 1946.
So, were these 244A or 244B? Anybody's guess! On page 118 we learn that four FA units (well, three FA and one FB) were built for GM&O with Auburn engines in January of 1946 (dates 9 January and 19 January, though when GM&O got them I don't know: 9 January was the release of the first A-B-A set for road testing on the D&H, 19 January the date given for the 702, which "was retained at the Alco plant and placed under extensive static testing.") There was then a pause (maybe even Alco realized it was wise to do a bit of testing before starting mass production!), and the next FA built (GM&O 703) left Schenectady in May. So the first Schenectady-built 244 engines were built before all of the Auburn engines went into locomotives.
Also on page 118: "Alco's tooling to permit building the model 244 engine at Schenectady was not installed in sufficient time [...] and accordingly the production of engines for powering these [GM&O] locomotives was begun at Auburn [...] 35 engines were built at Auburn. These engines were assigned McIntosh & Seymour serial #'s 4253 through 4286, and 4447."
(The intention was for Auburn to build 34 engines for the first 34 GM&O units, but the first engine built was diverted for use as a stationary lab engine, and #4447 was added to the Auburn work order as a replacement.)
Page 118 continues: "These engines were completed at Auburn between October 20, 1945, and September 21, 1946. They are listed in Auburn's records of construction as model 12-9x10 1/2 V-241 engines... Note that Auburn designated these 35 engines as model 241; when placed in locomotives at Schenectady, they were designated as model 244."
Page 119 has a table showing which GM&O locomotives got which engines in the #4254-#4286 series: FA-1 700 through 726 and 728, FB-1 B-1 through B5. (GM&O 706, whose builder specification card you have seen, got #4258.)
Sorry, not sure how useful that is! I'd guess that design up-dates were were being made on a continuous basis, and I don't see any obvious place for a "break" between 244A and 244B. MAYBE the first 20 Auburn-built engines were 244A (which would explain why the cost record in Steinbrenner's book is for the conversion of just 20 engines from 244A to 244B standard), but I don't see anything in Kirkland to confirm this.