Stainless fasteners often will tolerate more torque than the original fasteners, but what they are screwing into does not.
Here is a little about the physics of fastener torque.
Engineers don't think of fasteners in terms of torque so much as they think of fasteners under tension. Torque is simply a way of applying a measured amount of tension on a fastener. Thing is, there are a lot of variables as to how much tension a fastener will have for a given torque. Diameter, thread pitch, and material all play a factor in the engineer's calculations for how much torque should be applied to a fastener. These are all things that the engineer can control. What they can't control is a whole array of factors that we, as the mechanic, can affect. Surface contamination, thread lubricant, and fastener fatigue are all field conditions that affect how well a fastener will hold.
Think of a fastener as a spring. What keeps it tight, is its elasticity. The fastener and the components being fastened are under tension, and distort from the tension. If a fastener is over-tightened, it is like over-stretching a spring. It will lose it's original ability to hold tension. Thermal changes during operation can significantly affect the tension on a fastener system. (By "system" I mean the assembly of fastener, and the components being fastened.) A good example to illustrate would be a Harley Evo engine. When the engine is cold, there is inadequate tension on the cylinder/head studs. They are long fasteners, and the cylinder/head "stack" is quite tall and made of aluminum. The aluminum expands much more than the steel cylinder studs as the engine heats up. It is well known that hard acceleration on a cold Evo engine can cause cylinder base gasket leakage. They should always be run gently until the engine is warmed up and cylinder stud tension increases. The point I am making is that the desired tension on a fastener needs to be within a range that has enough tension to seal when cold, yet not overstretch the fastener at operating temperatures.
What are those factors that we encounter in the field that affect fastener tension? What should we do about them?
Fastener friction is a BIG factor in how much tension you have for a given torque. Engineering calculations require clean threads lubricated with oil. If a screw has surface corrosion and is installed dry, it will not have the required tension, and you might have leakage. On the other hand, anti-seize can reduce the amount of torque needed to achieve the required tension by as much as 20%.
In your case here, you are using a higher strength fastener than the original, and because the thread penetration is a lot of threads into the case, You can easily have more tension on the new screws than the original screws ever had. That is OK, but you don't want to crush the gasket.
ALWAYS use anti-seize on stainless fasteners. Stainless has a tendency to weld in place. (Usually referred to as galling.) This can make the fastener hard to get out in the future, often damaging threads on removal. Also, there should be a little anti-seize on the underside of the fastener head.
Most torque specs give a range of torque. If using anti-seize on any fastener, use the lower end of that torque range. There is so much less friction when installing the fastener with anti-seize, that it takes less torque to achieve the required tension.
As far as engine case screws and using stainless socket head cap screws, I skip the torque wrench simply because I have an experienced feel for how tight things should be. You would be surprised by how many fasteners get stripped or broken because the less experienced mechanic
was using a torque wrench. The torque may be given in in/lbs, and the mechanic sets the torque wrench to ft/lbs. BAD mojo! It's a more common mistake than you might think. Tool rental places have told me of guys renting a torque wrench, and not knowing that when the wrench clicks, you are torqued. They would just keep tightening until the head bold snaps.
Tighten your case screws in stages. It doesn't really matter whether you do a criss-cross pattern, or just run around the perimeter one screw after the other so long and you tighten the screws in at least 3 stages. I usually use a criss-cross pattern only on the final stage of tightening. Just use common sense. You can "feel" the elasticity of the fastener when you tighten. Just use the plain allen wrench without any kind of additional leverage. Try to make each stage of tightening as consistent and even as you can. Hold the wrench in a similar manner each time so that you can be consistent. For example, don't do one fastener pulling with your fingertips, and the next fastener by pushing with your palm.
Head bolts are more critical, and I always use a torque wrench on them.