There are few to no penalties for starting any crafting or gathering classes at lower levels, although higher level benefits do help. You will retain all your levels in your previous class and can switch back to it at any time without penalty. Any new class you obtain will start at lv.1 and you will have to use various means to level it up. Keep in mind the majority of quests are not renewable, so you will be grinding fates, leves, hunting logs, and dungeons for half of your battle classes. It is easier to level those classes because there is a 50% xp bonus associated with all activiites except questing, and cross-class skills and access to better equipment make you more survivable and hit harder.
The biggest limitation to crafting classes is gil. It can cost quite a lot of money to obtain all the necessary materials for crafts. At lower levels, many of your materials will be purchased from npcs. These are not expensive relatively, but you may still feel the pinch on your wallet. After Lv.15 or 20 though, you will become increasingly reliant on your own gathering classes or the marketboards for materials.
The marketboards require you to complete the Lv.17 main scenario quest, Scions of the Seventh Dawn. Doing so unlocks the retainer feature (which provides extra storage slots and lets you buy/sell materials on the marketboard). If you buy materials from the marketboard, be aware there are times when prices are low and prices are high. On Leviathan server for example, many players begin undercutting each other over the weekend. This means it is cheapest to acquire craft materials in bulk starting from Friday and it becomes progressively more expensive afterwards. You can also examine the marketboard's history and find items that are easy to get/make and sell for a good amount of money. Spend some time to learn the sale times for your server to capitalize on profit and minimize costs. The retainer isn't necessary for low-level crafting as you will likely be leveling simply crafting all the gear you will use (at 25% of the cost), but it is useful if you want to craft Lv.20 and higher items quickly and/or sell items to fund yourself.
If you continue your main scenario quests to Lv.20, you will eventually decide to join a grand company company. You can then earn grand company seals to buy a chocobo mount. This will provide improved map movement to help you travel to gathering nodes. It's not strictly necessary since the nodes are relatively close together, but it is more a matter of convenience.
As far as guides on mechanics go, that is a very broad question. Many of the issues are discussed in the relevant subsections of the forums, but I can't point to any site with a consolidated and cataloged database on everything you might want to ask mechanics-wise. A query using google will probably yield most answers, but that assumes you're using the right keywords and terminology in your search. As far as an introduction to those terms though... the new player subsection and class-specific subsections are the best places to pick those up. If you can't find the term you're looking for, your best bet is probably to post the general question or mechanic-in-question on the beginner forums and use the information and terms gleaned to catapult your search.