Here I will set out the rules which you should follow to make sue that you don't end up regretting countless dollars and hours spent on your car.
1. Know What You Want
There are at least couple of reasons why you should have your end goal in mind. If you've ever seen that modified car which looks like its going for 7 different looks ("it's a stance/rat-rod/track day/street-strip car brooo"), you'll understand the importance of having a particular goal in mind. The aesthetic reasons for this are obvious, but the importance of a solid purpose is even more apparent where performance is concerned. Improving a car's performance means much more than increasing horsepower and grip. Just buying the biggest tires and turbo doesn't guarantee success in any competition. A 10-second Miata isn't going to win in SCCA Solo, and a perfectly setup STS Miata isn't going to "gap" anyone on the street.
This kind of focus also has financial benefits. The cost of meandering modifications increases exponentially as the car changes. This makes the difference between looking at your car as a financial black hole and hard-earned money well spent.
2. Have a Plan
This may sound like this first rule, but there's an important difference. Oftentimes, knowing where you're going does not make it clear how you are going to get there. Should you go turbo first or buy those coilovers? You know how much horsepower you want, but will it kick you into a non-competitive class? This may be determined by the way the car is used. Modifying a daily driver on weekends is going to look different than a dedicated track car. Finances will also influence the way modifications are applied, and having a specific timeframe and order in which you'll be working on your car will make the process less of a headache.
3. Have a Budget
It's easy to go from Christmas morning excitement to remorse when you see the bill for all those parts show up on your checking account balance. But if you know ahead of time what you'll be spending and when, you take the emotional rollercoaster out of the equation. Instead, buying racecar parts will be the glorious experience God intended it to be.
The Two Budget Methods
There are two ways to come up with a budget. The first is to figure out how much you can spend, and see what you can do with your budget. You know what you want, you know how you'll get there, and you know have much you can spend. This is the more responsible--and correspondingly less fun--way of setting a budget. The second, more appealing way of coming up with a budget is to reverse engineer your plan. First you figure out how much your plan is going to cost, then you let your income and expenses determine when you'll be able to take a bite out of your parts list. The first method gets your car finished faster, the second helps you take your car to the next level--albeit next year.
4. Do Your Research
You need to do lots of reading. I know how much reading you think I mean, but I actually mean much, much more. You're reading this now, and you've increased your estimate, but it's still too little. It's not an exaggeration to say that you'll likely spend more time reading than wrenching. Research doesn't mean posting on forums. In fact, most forums have been around long enough that asking questions is almost entirely unnecessary. Unless you're doing some wacky swaps or using unusual parts, it's most likely been asked before. This is especially true of popular or longstanding models like Miatas.
If you don't know where to start, you should lookup the projects or builds section of the forum, and start reading through what other people have done. This will certainly get you the kind of information and inspiration to get you off the ground.
5. Know the Consequences
No matter how well you plan and how careful you are, modifications will compromise certain aspects of your car. Adding power will decrease mileage and most likely increase wear and tear, stiffening your chassis to reduce body roll will make the ride harder, and before you're done, you may come to the realization that you're driving a loud, stiff, uncomfortable car to work. So make sure you know what your car will really be like when you start bolting shiny bits to your daily driver.
Modifying a car will always bring some risk and uncertainty. The process often includes a fair amount of trial-and-error. But that's par for the course, and if you make sure that you know what you want, and you know what you're getting into, your experience won't be so terrible that you resort to warning noobs against turning a wrench.