Hi! You’ve already heard my answers, but I thought I would post here with the community to see what others think.
I highly recommend playing through at least one event, and ideally an entire scenario, before making changes to the rules. This will give you a good feel for the system.
Fate of Cthulhu scenarios consist of four events. Each event takes 1-2 sessions to go through, concluding with a major milestone (in Fate Condensed terms, a Breakthrough with both optional advancements included). As such, if you stick with the rules as written, characters will go through three major milestones before reaching the 4th mission, eventually giving them a total of 3 additional Refresh and 6 more skill points.
1) Increasing the refresh from 3 to 4
How long do you plan to run each session? A Refresh of 4 enables players to buy an extra stunt right away, or have a lot more ability to invoke Aspects before feeling pressed to accept compels.
This is a pulp horror game, and you may remove some the tension this is meant to create. More stunts = more power, which may also deter characters from using corruption stunts.
2) Increasing the Stunts from 2 to 3
Increasing the Refresh or increasing the # of stunts is roughly equivalent. Doing both increases the impact of the changes listed above.
3) Increasing both the Stress boxes by 2
Fate Condensed (and FoC) have added flexibility by allowing players to tick multiple boxes of stress, but each box being worth only 1 stress. Players can already increase their stress boxes through high physique and will ratings up to 6 boxes.
This will lengthen fights, and reduce the difference between characters who choose to invest in high Physique vs other skills (somewhat devaluing Physique depending on the challenges you throw your players)
If you are worried about how squishy PCs are, it is far easier to control the toughness of adversaries and obstacles. If you find out you underestimated the toughness of your PCs and encounters are too easy for them, far easier to throw in an extra adversary in the mix, or compel PCs to throw in complications (which also favours them with a Fate point)
4) Fate Toolkit Pulp Skill Pyramid - +5 to +1 (with five more skills)
You are basically giving an extra 15 skill points to players. If you start PCs with such a broad pyramid, there will be more overlap between PCs. This is a huge difference. If you play the scenarios as written, you will likely find they blow through them easily.
As a Fate GM, you should be a fan of the players. You should discuss with them the tone of the campaign they are seeking. You can have a more hopeful tone and have them completely prevent the Arrival, but you also want them to feel like they earned it.
Ultimately, whether you choose to play with the rules as written or hack it: as long as you and your group are having fun, you are doing it right!