Geez, I went down this path before, and I made some silly decisions. Okey, the first rule of thumb is - if you intend to sell your guitar sometime later....don't mod....period. Because you will be wasting lots of money, not forgetting your time and effort. Buyers of your used guitar don't care about your mods. In fact, some may be put off by it. And don't even think of pricing your guitar higher because you think it's an upgrade. Buyers don't care, and your upgrades may be another person's downgrades. But if you die die have to mod, then make sure it's reversible and always keep the original components.
For me, I will mod and upgrade my guitars regardless of the price tag. Because of itchy backside, I even did an extensive upgrading on my Gibson LP Custom....which is sacrilegious for some!
IMO....if budget is not a factor, it's best to start off with a
mid-level guitar (at least $400 and above) to mod or upgrade. Spending too much money to upgrade a cheap crappy guitar is just not worth it - ie. guitar that comes with low quality wood, dead sounding wood, bad fret job with sharp edges, lousy hardware or poorly drilled holes.
You can only improve your guitar to a certain extent (in terms of tone, versatility and playability), and a cheapo guitar usually has its limitations. That means....would you spend your money to improve on a poor quality instrument, so it can play decent and sound average? For me, it's not worth it.
However, the upside of modding/upgrading is....the sense of
satisfaction and
achievement you get when you transform a good guitar to a
great one (to you at least). It's something an expensive stock guitar can't give you! And a modded guitar also has your personal flavour and touch all over it.