I'll start with the CI strats. I don't think they work, it's just that I'm not sure what happens when you do certain things on the level. I'll start with PA.
Start, open the hologram room, enter the last lift. Save all 4 hostages, get the devastator. Destroy the safe and get in the other lift. Blow up the glass as you approach and hop down. Activate the guns and uplink the ship when you "pass it" / get to it. Go up to the firing range and complete the hostage objective. Get the rcp120, leave, jump where the glass was and go to the exit.
I'm not sure what uplinking early will make the game do with the speech at the end. For SA it would be the same IF the ship would be there. On PA the ship comes after you destroy the safe, but I don't know about SA.
Very unsure about that strat... need some tests done.
Investigation - A, SA. Many people who have played PA would know you can get fast bots - up to 127. On PA you do 2 things different to SA before you notice that the bot is fast - Get the K7 and operate the camspy from far away. Ryan and I tested going into the K7 area on Agent and it did bugger all, so I've decided that I think it's the operation of the camspy from afar that does it. This is what you would do on SA:
Go like normal until the camspy first part. Simply deploy it and leave it. Do the first experiment then while you stand at the computer, move the camspy up to the isotope and take the photo. Go do the experiment furthest away. Stand at the computers and switch to camspy, move it around for all the time you can spare (and still catch a 12

. Get the last experiment and go to lasers.
The logic in this is good. Perhaps operation of the camspy in the K7 area would be good.
For agent, just deploy the camspy, go "somewhere" and play with the camspy for all your free time, so that you can still catch a 46 bot.
No idea if any of these work, but the logic for inves is good, and the rewards for CI would be great if that works. Might as well give them a shot.