quote MagmaTyphlosion X

I have another question: Is it preferable to save at every checkpoint you reach in the game, or is it better to save at intervals (e.g. every 2 to 5 checkpoints) since saving can cost a few seconds?

Ok a few tips that may help. In no particular order as i am just typing them as i remember lol.

empty your starting gun's magazine you will need it to speed up (slightly) the scene before you met MKII, i forget the name but you start crouched behind a wall, 2 pmc's are awaiting and a truck with more will follow.
If yu throw the magazine then sneak past, then run around the outside to avoid the truck.

It's easier to see on a you tube video than to explain, but it essentially cutso our about 10 or more seconds of cutscene + it gains a few seconds on the playtime.
When you meet up with mark II you MUST stun.knockout the three pmc's outside in full view of the rebels, otherwise the next part is harder.
5f you do that correctly you should gain a neutral rebel status so you can run through (more or less) militia safehouse.

Don't help the rebels again until the second phase of act 2, it will only slow you down.

Biggest tip i would say is that you have to be speedy on the boss's, for example dont use the snipe/truck method for wolf and dont use the lying on the stairs snipe method for raven.
Wolf can be beaten in about 1min 10 seconds including her beauty phase if you do it right, raven under a minute.

Make sure you have enough chaff grenades and use them at the helipad on SM, you can sneak through but it's easier and faster with the chaff (hint though you really need a minimum of 3 chaffs to do big boss run very quickly)

Another tip when the MKIII is opening the door on SM get out the Railgun, charge it and destroy the gekko, saves time waiting for it to open the door.

for vamp do a fully charged/auto aimed solar gun into him, he is the quickest boss to dispatch, way under 1 min.

For the next gekko scene loose the railgun and switch to the M82 its MUCH quicker, also lie down and play rock me baby, or sailor on your ipod

You asked about saving after every checkpoint, i did and i got 3 hous 27, not an absolutely brilliant time but im happy with it.

Basically just kep replaying the levels until you have it streamlined, find out what you can get away with and just shave second by second off until you have the fastest run you can, just go into each level saying i need to shave 2 mins off, then you will be in good standing.

Best of luck with it