These are the notes I used for my 4:17:54 run. They might not be the best tool to learn though, since they're pretty bare.
(I have updated the notes several times to incorporate new strats and findings.)
[Mission 1] Quit to Main Menu after the first "loading", load Autosave Create Savegame (for cutscene skips) Cutscene Skip Bartender, Juni+Diplomat Take Mission 1 (cutscene skip) Sell Bats & Bots Buy Javelin + Ammo Kill Order, fly to Fort Bush Lane once dead and dock asap Form up with USV Brandt Kill Rogues, use Tradelane as soon as USV Brandt is within 2000m of the lane Dock at Pittsburgh, load savegame, Undock from Pittsburgh asap (cutscene skip) Form up with LSF Fighters, defend XT-19 Fly towards Manhatten, stay within 2.9k of the Waypoint till Beta-4 Comm Fly towards the Particle Cloud, rescue Beta-4, continue to the cloud Shoot down Weapon Platforms, head for Pittsburgh
[Freetime 1] Dock on Pittsburgh, buy Rhino + Stunpulse Turret, undock Loot DSE H-Fuel Depot as Fort Bush Fly to Manhatten, sell H-Fuel+crap, buy ammo, buy Justice guns/turrets Accept Mission 2 (cutscene skip)
[Mission 2] Cutscene Skip Lonnigan Fly to the Colorado Gate and use it - make sure King follows you through the Trade Lanes, as he is required for the Unity Trigger Fly to the waypoint and then to the Tradelane to Pueblo, scan DSE - Unknown as soon as you see him Take out Kosmo, dock with the Trade Lane as soon as "Game Saved" appears (King has to come with you) Take out the Rogues, fly towards Ouary asap Take out the Rogues, weaken the last one and fly towards the NY Jumphole Get within firing range of Ashcroft, use EK to kill him Fly to NY, when flying to Fort Bush make sure King comes with you, as he is required for the Rouges Trigger Fly to the Rogues, aggro them on you and kite them towards the H-Fuel depot take out all containers as long as there is an enemy within 2.4, otherwise only 2 Fly to Missouri, dock and cutscene skip
[Freetime 2] Sell 16/48 H-Fuel Fly to Fort Bush, plunder the H-Fuel Depot Fly to Manhatten, do cutscene skips Fly to California Minor, load Autosave after jumping Buy Slingshot Missile, Lv. 3 Shield and Heavy Thruster Accept Mission 3 (cutscene skip)
[Mission 3] Undock, fly to the Magellan Gate and head to the position where the Transporters spawn (left of the Rheinland nebula) Stay close to the Transporters until the 3rd Buoy Take out the Outcasts, head to Willard as soon as the last one dies Dock, sell H-Fuel, Undock Directly head to California Minor Docking Ring Take out the Rheinlanders Fly to California, go into EK to get rid of Juni, dock with California Minor Enter the bar, skip the cutscene Undock, Fly to Walker, Fly to Willard as soon as the game acknowlegdes that you were at the Waypoint Take out all Rheinlanders (if you're fast enough you can take them out before the Bomber spawn, but softlock risk!)
[Freetime 3] Fly to Manhatten Sell crap, buy H-Fuel, buy Ammo Undock, load Autosave Accept Mission 4 (cutscene skip)
[Mission 4] Undock Stay close to the Trade Lane towards West Point, dock with it as soon as possible Make sure King and Juni come with you Thrust through West Point and dock with the Trade Lane to Ithaka Make sure King and Juni come with you, as they're required for the Benford Trigger Fly towards Benford Do whatever you want, except dying - your position will be reset after the Cutscene Fly to the Magellan Gate and dock with it ASAP (go in EK at a distance to get rid of Juni) Fly towards Mactan, Attack the Bounty Hunters as soon as you can (even when they're neutral) Fly to Mactan and dock with it (don't repair if you want to go for the repair Tobias cutscene skip) Undock, kill the Rheinlanders, head to the Leeds jumphole Fly to Planet Leeds, dock with it Repair your Ship, press F1 until you hear the dealer menu open (-> Tobias Cutscene Skip) Alternatively do the normal Cutscene skip but do NOT load the Van Pelt savegame!!!!!!
[Freetime 4] Buy 80 Optronics, sell 45 of it, Buy 35 H-Fuel, Buy 2x Adv. Stunpulse, Imp. CM Fly to Battleship Norfolk Sell H-Fuel, buy Crusader, default shield and garbage, buy Lv 4 Shield, another Slingshot, Lv 4 Weapons and Ammo Fly to Camebridge, sell Optronics, buy Diamonds Accept Mission 5 (cutscene skip)
[Mission 5] Undock, Follow the Waypoints until you Reach Freeport 1 After leaving the Tradelane, fly directly to Sprague Take out the Rheinlanders and dock Undock and fly directly towards Baxter and dock with it Skip the cutscene Undock, kill the Rheinlanders and fly directly to the Camebridge Hole Fly to the Waypoint until the 2 Rheinlanders appear Fly to the Leeds Hole, don't stop Kill the enemy Rheinlanders, dock with the hole Fly directly to the Tradelane, which gets marked (only this one ring works!) Dock with the Tradelane, dock with the Planet Cutscene Skip
[Freetime 5] Sell Diamonds, buy Mining Machines (also sell garbage) Fly to the Hood Sell Mining Machines, buy Gold, but Torpedoe, buy 1 Catapult, buy ammo Accept Mission 6 (cutscene skip)
[Mission 6] Undock, win the race, dock with the Hood Undock, fly to Glorious directly Kill the Rheinlanders, dock with Glorious, load savegame (cutscene skip) Undock, head for Waypoint 1, kill the Rheinlanders head for the Leeds Hole and kill all Rheinlanders on the way Use the hole, fly to Planet Leeds and Dock Accept Mission 7 (Cutscene Skip)
[Mission 7] Undock, kill one Agent, use the Tradelane ASAP Kill the Rheinlanders (2) until they cloak, use the Tradelane to the Gate Kill the Rheinlanders, dock with the gate ASAP Fly to Holman and then directly to the Tau 29 tradelane Fly to the in construction ring for the Tau 23 Lane as soon as the Battleship uncloaks Dock with the lane ignore the corvettes, Fly to the Jumphole, dock with it and head directly to Shinkaku Dock and Undock, fly to the point of the Schiller Battle directly Take out the Schiller Fleet and head to the Tau 23 hole as soon as the last enemy dies Fly to Cali and dock, skip the first cutscene, enter bar, skip the second cutscene Fly to the Kyushu hole immediately Land on Kyushu, Cutscene Skip
[Freetime 7] Fly to New Tokio Sell Gold Buy Barracuda Buy Light Weapons Fly to Shinagawa Accept Mission 8 (Cutscene Skip)
[Mission 8] Fly to the Honshu Gate Fly to the Honshu Hole Fly to Yukawa Shipyard, take out the platforms and fighters Go into formation with the transport Take out the Marine fighters, Fly to the Chukogu hole Land on Kyoto Cutscene Skip
[Freetime 8] Sell Light Weapons, sell garbage, refill ammo Accept Mission 9 (Cutscene Skip)
[Mission 9] Fly to the Tohoku Hole Fly up to 5K distance to Outpost Ryuku Fly to the arc, kill the patrol encounter Take out the generators Do the rest of the mission fast Cutscene Skip upon landing on Kyoto Accept Mission 10 (Cutscene Skip)
[Mission 10] Undock, fly to Sigma 13 Kill all 8 fighters (or 4 cruisers or 1 battleship) Head to the Wrecks and loot them Fly to New Berlin (Cutscene Skip on landing) Fly to Holstein, get rid of Fischer with EK to dock before him (NO Cutscne Skip!) Fly to Bruchsal, defend it, land there and skip the cutscene (don't load the last mission save!) Sell Wreck Loot, buy Luger (4x, for later) and a Driller Mine, buy Ammo Undock, fly through the passage and destroy one experimental ship Wait until Botzler dies, then fly directly to the Hamburg hole (stay within 6k of von Claussen until Botzler is dead) Fly to the Waypoint, dock with the Osiris once the goal appears Accept Mission 11 (Cutscene Skip)
[Mission 11] Buy an Anubis, buy Debilator Turret, buy mines, sell garbage Fly to the NY Hole and dock Take out the Liberty Ships Fly to Buffalo and dock (cutscene skip, "Mission 11: Buffalo Base") Undock, fly to NY Jumphole, Fly to the Satellite Take out Satellite and fighter, head to Walker Form up with Walker (you need him) Kill the fighters until Juni enters the code, dock with the gate ASAP Fly to Mitchel, go into EK at ~4.5K distance and Dock Fly to the NY Gate and stay close to it, dock with it as soon as possible Fly to the Omaha, wait for the Osiris to uncloak and dock with it Accept Mission 12 (Cutscene Skip)
[Mission 12] Fly to the first generator, wait until it's damageable Destroy the 3 generators Fly into the Nest and get the Energy Cell Fly to the hole as fast as possible and dock with it Head to Toledo, ignore the Nomads Accept Mission 13 (Cutscene Skip)
[Mission 13] Cutscene Skip Destroy the first battleship (head left) wait for the docking order, dock, cutscene skip, undock Fly to the Osiris immediately Dock, cutscene skip, refill ammo, Undock Fly to the Hyper Gate immediately destroy the nomads, dock with the gate ASAP fly to the entrance, destroy the 4 generators fly through the entrance fly to the first generator immediately destroy the generators