A few thoughts:
Bitter Jeweler -
Bitter Jeweler | Photography Forum - search through that guys threads, he's done just what you have. His earlier threads back when he started might have some good content and some of his latter more details on this kind of photography
1) ANY DSLR will do this kind of photography and do it well. Differences will be minor between the various models so honestly I would say that you can pick and choose any current DSLR from pretty much any company - although Canon and Nikon are the top choices.
2) You will want a macro lens capable of "true macro" which is generally defined as when the lens has a reproduction ratio of 1:1- that is when the size of the subject reflected on the sensor by the lens is equal to its size in real life.
Note that most lenses with a single focal length (primes) with "macro" or "micro" in their name will do this. Zoom lenses with macro/micro are generally close focusing only and whilst good will not do such a high level of magnification.
3) Lens wise I would suggest a lens of at least 60mm in focal length and any limit on the longest focal length (although practically speaking I would say 105mm is the longest you'd need). With macro lenses the focal length affects the working distance, which is the distance from the front of the lens to the subject*; with longer focal lengths having a longer minimum focusing distance and thus generally longer working distances. 60mm is around where the cut-off point is for practicality at 1:1 magnification; any shorter and lighting becomes a real problem and 90-105mm is a general "sweet spot" of ranges good to start with.
4) Lighting is KEY for this kind of work. You'd be best to library loan/buy a copy of "Light science and Magic 4th edition" as a starting point. At its most basic you want big light sources relative to your subject so that the light is diffused well; there are also key elements regarding shadows, reflections and the angle at which you set your lights (hence the book recommendation). Thus chances are you will want to look into things such as:
a) Light boxes - essentially a box with white paper walls which has the subject in the middle of the box; flash/constant lights then shine in through the paper and the paper is (relative to the subject) the light source - and being much larger is thus diffused
b) Softboxes - essentially a box with a white screen front and a flash put in the rear; again its like the light box in that it increases the size of the light source relative to the subject. Bonus is that with a couple of softboxes and stands you can move them around more freely.
Lighting is a curious area as you can do a lot with very cheap setups. I would suggest looking into at least:
1) Two speedlite flash units. You can get studio flash units as well which will give you more power for your money; but at the same time they are larger and quite honestly for this kind of work they are overkill - speedlite flash units are more mobile and thus can also be used on the move with other photography should it take your fancy (most studio flash units require mains power or heavier battery packs - there are some mobile options but again its overkill and they are very expensive for the mobile versions).
2) Two softboxes - or a light box - a bit of a personal preferences aspect this one and you can read into loads of different setups (the book is helpful at giving you some guidance and you might find reading it confusing at first, but its well setup for beginners to get some grounding which might make your choices easier to make).
Note that ideally you will want some stands too; bigger softboxes tend to come with them as part of a kit; smaller ones might not but you can get cheap stands for not much cost - second hand (
ebay) tripods also work well for this (tripods tend to devalue fast - even the good quality heavier ones). Note avoid the ultra cheap aluminium tripods (the cheap ones sold in most shops) as they are just too cheap and lightweight.
3) With the flash units you want a wireless radio release system. Thus means that you can position the flashes where you want and trigger them; without a cable getting in the way (there are wired systems and if finances get tight you can use wired as it is cheaper).
Canon currently has built-in wireless in their top of the line speedlite flash the 600EX however the cost of two of them plus controller for the camera is rather high for what you need. Cactus is a company that makes 3rd party wireless remote triggers and are generally considered good for a cheap and practical option - Pocket Wizard are the leading manufacturers; but rather like the Canon Speedlite option, its going to be most costly.
Camera and lens wise:
a) Lens wise I'd suggest looking at the Tamron 90mm f2.8 macro; Tamron make it in a variety of mounts for different DSLR bodies and its a generally considered great choice for getting into macro. The Sigma 70mm macro is also a good choice and if you can find them the previous version of Sigma's 105mm macro is good (the newer is mostly adding OS which you won't really need for this).
b) You will want a tripod, Manfrotto make some good choices and their 055 series are a good quality affordable brand line.
c) Along with the tripod you'll want a tripod head (good tripods separate head and legs, but you can often get legs with a head in a kit). The best for this kind of work is the Manfrotto Junior Geared Head - its costly but really shines in macro work and if you're doing macro work a lot its really the head I would get. It offers fine toothed control in each of the 3 axis; its a slower head to use (you can't really pan or do action work with it) but for macro it really shines.
d) A macro/focusing rail. This lets you move the camera and lens back and forth; which is often how you take macro photos (you set the focus and then move the camera and lens to get focus; since AF tends to be rather poor at macro work**). The small distances a rail lets you move back and forth are much easier done than trying to move the tripod back and forth to get the same effect (although on a firm indoor floor its possible - outside or on carpet/rumpled ground its very hard).
There are good cheap rails on
ebay which are good enough; manfrotto also makes one though I'm not a fan of their design. Velbon also makes a good quality rail (oft sold on shops or ebay).
*different to the minimum focusing distance which is sensor to subject distance
** some of Canons newest cameras such as the 7DMII when coupled with their newest 100mm f2.8 IS macro can do a much improved job; but that setup is expensive and, honestly, your rocks are not going anywhere so you don't need the AF
edit - PS - on your second photo your friend has "dust bunnies". Those dark dots are dust on the sensor, which shows up when using small apertures (big f numbers). They are easily removed with the "spot heal tool" in photoshop and lightroom (note you can get both those software packages from Adobe for a very low monthly subscription cost now - worth looking into).
Sensor cleaning can be done in nearly any good photography shop or you can do it yourself (lots of guides out there). Sensor dust is part of digital photography and you won't avoid it totally - however in general its easily removed and if you get it you can clean it off so its something to be aware of but not worry about.
Note a clean white sheet of paper with a small aperture (big f number) is the best way to show up sensor dust; complex scenes will hide it and wide apertures (small f numbers) won't show it.