I've just reached New San Francisco with the Fob Key and the Nav Module. I'm wondering, because I'm reading ahead in the walkthrough I'm using, exactly how I should kill President Richardson, and how high my Speech score should be in order to convince Murray to destroy the base (my Speech is currently 100%, but even that wasn't enough to get past the Commander's Guard speech check for the Fob Key; I had to kill him).

Thus, how many Super Stimpaks would I need for the assassination (or, how much health does Richardson have), and how high should my Speech skill be for the end?
Alright, I have another question about the endgame. I had to kill the Navarro base commander. Will I have to fight my way through the Oil Rig?

7 Super stimpaks is enough for president.
You won't have to fight through the Oil Rig as long as you go in alone and nobody sees you without Power Armor.
99% is enough for Speech check, I just tried it.

The hardest speech check is just before the end when you can convince some powerful guys to help you in the final battle. I think I had about 126 speech skill and 50 percent success chance there.

You don't have to exploit the super stimpak cheese, you can slaughter the president the direct and honest way. You can also leave him alive and win the end fight nevertheless, in my game I destroyed the turrets when I first arrived. Even just slaughtering everything you meet works.

Don't take too much stuff with you to the oil rig, you might have face the "too many items" bug or slowdowns. You don't need more than one weapon and ammo for it, leave holodisks, secondary weapons and other stuff which won't help during combat (including the GECK) on a shelf or elsewhere.

I made it to the Oil Rig.

I left Marcus on the boat, and I'm wearing Advanced Power Armor, which I stole from Navarro at the beginning of the game.

My speech skill was raised to about 126%

I have the .223 pistol with a ton of ammo for it, as well as a Desert Eagle .44 with 200 rounds, and the P90 with some ammo. I do have a lot of extraneous items like flares and a water chip, a shovel, and the GECK. The last perk I took was Strong Back, so I have an extra 50 lbs of carrying capacity.

Don't overwrite your save game from just before leaving for the oil rig so you can try other things later.
Flares, water chip, shovel and GECK are useless there, you won't need the .223 pistol or the Desert Eagle .44 and their ammo either, you'll find enough ammo for your P90 there.

There's so much stuff you can pick up at the oil rig, it doesn't feel good having to leave so much stuff behind. My advice is dropping the useless stuff you brought with you right now, it will save you a lot of time for inventory shuffling.

Don't do this, I did this mistake one time. You'll never see Marcus again if you make him wait there, believe me. Make him wait in this room.

Unless you mean that you left Marcus inside the boat, in San Francisco, before going to OIl Rig. If that is the case, you'll be able to make him join your group again.

I left Marcus before using the computer to sail towards the Oil Rig (in NSF).

I completed the game:

-I stealth-killed Richardson for his passkey. It took me a few tries until surrounding guards didn't hear me hit him with the M72.

-I convinced Murray to release the FEV into the air vents and blew up the reactor with the Plastic Explosive

-I convinced Sgt Granite to help me fight Horrigan. I was unable to use Richardson's key on the terminal despite having a 70 Science skill and 9 Int. No matter, the turrets did nothing to me. This still took a few tries, as my Enclave allies were slow to get Horrigan's attention. I finally stood by the console and started firing at him, which got them to fire at him as well. I didn't think I'd make it after Granite was sliced in half. Three Enclave troopers survived.

I did not opt to continue playing.

What a fun and at times extremely difficult game!

Congratulations! : )
I highly recommend that you install Restoration Project next time you play Fallout 2. It corrects a lot of bugs and bring stuff that was intended to be in the game, but was removed (for lack of time, I think).
killap's Restoration Project

Or, if you just want a patch to correct bugs, install unofficial Fallout 2 patch.
killap's unofficial Fallout 2 patch

I installed a few mods: The High Res patch, and either Killap's patch or the Restoration Project. Can't remember which.