From: Zagreb, Croatia
I did a lot of counting the divisions - and as a result, the Germans have been beefed up a bit. The main points being including all the second rate units, including the border guard, as militia, beefing up the submarine strength in a major way - Germany actually did field seven U-Boat flotillas at the start of the war, although one of them was a training fleet, and adding a bit to the strength of the Luftwaffe.
Germany started the war with 57 submarines in commission (32 of them were coastal types, 18 were standard VII type, 7 long range IX).
In comparison, on May 1st, 1940 Germany had only 48 submarines in commission (29 coastal, 13 medium, 6 long range).
On June 1st, 1941, Germany had 139 submarines in commission (43 coastal mostly employed as school boats, 73 medium range, 23 long range). Note that at least a third of commissioned submarines (those not employed as schoold boats) were in training before becoming operational.
On May 1st, 1942, Germany had 302 submarines in commission.
Finally, on July 1st, 1943 Germany had 426 submarines in commission.
It is obvious from these figures that Germany needs no "beefing up" for 1939 scenario.
What needs to be beefed up is Italian submarine arm. Italians started the war in June 1940 with more than 100 operational submarines, a few of them based in Indian Ocean.