The best way to start is to make a long term plan that you will stick to, and a key part of that is to be realistic about how much you want to spend, then gear the approach to maximze HP/dollar. Set a realistic goal; a genuine 400-450HP is serious power and it won’t be a matter of slapping some parts together; most folks with SBC’s can’t even get there. Not trying to discourage; you might be surprised at what getting an honest 200-250HP out of a 3.1 would be like, you would surprise a lot of people.
There are two basic ways of increasing the amount of fuel and air burned per unit of time. Force more in (i.e. boost) or spin the motor faster. In this case (as with most small motors) by far the better value as far as HP/dollar is concerned is with boost, I’d go that route.
The internet is a powerful thing, use it. The 60 degree V6 was used in A LOT of cars, so even if whatever chassis (Malibu?) you have may not have a performance following & subsequent gearhead forum, others like the 3rd & 4th gen F-bodies and S series trucks do. You can find some veeery interesting things on the V6 forums. I recommend
Http://www.thirdgen.org Personal experience is really the second best teacher in some cases; others’ experiences are the best, since it can cut down on needless duplication of trial and error.
If it were me, I'd start with a rear mount low pressure turbo in the spirit of what STS sells. This way you don’t need to mess with turbo manifolds & related fitment issues. This would be the very first thing I’d do, since it should produce the single largest jump in power (and is a HECK of a morale lifter). The beauty of boost is that with a properly sized turbo it basically fattens up the power you already have, since all of the things that determine the characteristics of the motor—intake, heads, cam, are left as is, your just forcing more air in which basically will make the motor feel like a bigger version of itself. I'd start at about 5-7 PSI, and use one of the many free DIY tuning softwares out there with a wideband. Don’t underestimate the amount of work it will take to get this far. Once I got the tune right, I'd start creeping up in boost, though with stock internals, I'd self impose some limit like 10 PSI (just based on my gut feeling). At this point, if I was still into going on with the project, I’d consider going into the motor to upgrade internals & port heads, then fab up an intake, etc. so I could run even more boost. If you've not done it before, I highly recommend you price out machine work like a bore/hone, decking, line boring mains, balancing, etc. This is not a place to skimp.
Power is produced by burning fuel and air. Increasing the amount of fuel and air burned per unit of time increases potential to make more power. So, you want to flow more fuel and air. Since flowing more fuel is by far the much simpler matter, the difficulty is typically focused on flowing more air. This is the job of the top end of the motor, the bottom end must simply withstand it—a stronger crank, rods, and pistons won’t produce any more power, they’ll tolerate more power. I wouldn’t immediately delve into a bottom end rebuild.
The best motors are the ones that have a combination of parts that work together effectively, or compliment each other, if you will. Can’t stress this enough. The 3.1 is evidence of that--its just that its set up for low end torque, and has long narrow intake runners, small ports & valves, and small log style exhaust manifolds. They are all matched pretty well, as evidenced by the 3.1’s relatively fat low RPM torque curve. Put on a big high flowing custom fabricated intake, & you might gain a few HP higher in the RPM range, but it won’t offset the loss of bottom end and probably make the car slower if you do not also upgrade the heads & exhaust. A wise man once said, think of the engine as sections of garden hose. Even if you replace all but one section with a larger diameter, you will still only flow as much as the smallest section. You have to improve the entire system. If I chose to upgrade the intake, cam, and exhaust I’d build them around whatever you can get out of ported stock heads flow characteristics are, since they will be your ultimate limiter. What can you get out of the heads? I have no idea, I've never built a 3.1. The pain of building something uncommon is *you* are the R&D dept.
Once you hit a certain threshold of power, you will start fragging stuff like the rotating assembly, transmission, CV joints, etc. I’d mostly worry about the transmission, presuming this is in a transverse FWD application. At what threshold? The R&D dept will need to find that answer
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Good luck and have fun