1) I'm (mildly) OCD, so all of my divisions have to be sequential (i.e, 1 - 2 - 3 - 4), not just in number, but in organization so the First Army Group is Army 1, Army 2, (named appropriately of course), and the first army is 1st Division, 2nd Division, etc. So I have to rename* almost every division I start with.
2) After the Army reorg, I delete the Air Force (moving all the planes back into the stockpile).
3) Next I send all of my Task Forces to my main naval base before merging them together (that way the faster Destroyers stop using fuel when they arrive instead of being slowed by traveling with the BBs and Submarines.) Eventually I will split them by role, so a Carrier Stack, BB/BC stack, CA, CL, DD (usually multiple for Screen, ASW, Escort, etc.) and an SS Stack. Once everything is grouped I exercise them starting with my Subs, then small groups of DD, etc. I try to keep my groups at a size that I am still (slowly) filling my silos and once full just less than my daily gain.
4) After that it speeds up: Research, Military Contruction, Civil Construction, NF, and such are quick because they rarely change.
All told it can take me up to an hour for a larger country like the USSR, UK, US, or Japan. Never really play France, but it would probably take a while as well. Germany is actually pretty fast since it starts out so compact.
* I have custom namelists that have the divisions in order, are all cross linked (so I will never have a 1st Infantry, 1st Mountain, and 1st Airborne at the same time...and I don't get anal about making sure the 81st division is always the 81st 'All-American' Airborne Division). Some countries have special exceptions (i.e, Italy and Germany have separate lists for Alpine/Mountain troops), Cavalry and Armor are usually different lists (from infantry and each other), I don't link the German Panzergrenadiers, but do link the Italian Armor (as far as I can tell Italy didn't have separate sequences for anything except Alpine and Cavalry, they might have reserved numbers/sequences for the different types but they didn't overlap.)