Pedro Claro
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I've been taking photographs of mushrooms for over 10 years and I tried a lot of different things in this time span.
I'll start by commenting your questions and doubts...
First, I think all advice about composition that was given to you was pretty valid. If you do real close-up work, a centered mushroom will work fine (its own structure will spread well in the image), as said by Kenny, otherwise it's better you try to follow the thirds rule. Also, your first two shots are not leveled, which IMHO do not contribute to a ballanced composition. The closer shots vs. wider shots is just a matter of taste - I strongly disagree with gardenvalley in that matter  - and you can watch Taylor F. Lockwood's work and see magnificent straight-on photos of mushrooms without finding them boring (see http://www.taylorlockwood.com).
Regarding aperture, I wouldn't recommend such small f-stop values due to diffraction. When I used APS-C cameras I tried to keep the aperture between f/8 and f/11 (eventually f/13) and only in the extreme need to get more depth of field I dared to go down to f/16. Now I shoot with a 5D and I have no problem using f/16 or close a little more, but f/32 wouldn't be my choice. Also, I don't think you'll need to gather the whole mushroom in focus to get a good picture; you can work with bigger apertures and selectively shoose which parts get in focus and which ones get out of focus. The DoF preview button is immensely useful for this...
If you're getting strange artifacts when using bigger apertures, I guess it may be a lens or camera problem, but it certainly is a strange thing to happen.
Finaly, regarding flash, I understand why many people don't use it - harsh light, unnatural look -, but (pardon my immodesty) I believe it happens because most people can't use flash properly. I always use flash, because in deep forests light tends to have a unpleasent magenta cast and not always it's possible to use reflectors to redirect some light to the darker parts of the mushroom (namely under the cap). Used with parsimony, flash can give you all the light you need, render better and more natural colours and even create a mood.
So, here's my method and 'workflow'...
I always use a tripod for critical work (besides taking photographs, I'm also scientifically interested in mushrooms, so I may only take a 'fast' shot to document what I see); I use a Manfrotto 190 with a 410 Geared Head, which is a fantastic tool to allow precise composition - it's not essential, but it helps a lot.
I always use Av - because it is more useful to control aperture (Depth of Field!) than speed and because this way flashes behave like I want (get there in a minute).
I try to compose according to what I have (a single mushroom vs. several mushrooms; big vs. small; a close portrait vs. a more 'environmental' shot) being careful with the manipulation of the mushrooms (usually very fragile) when taking apart small branches or leaves.
I select the apropriate aperture, according to my 'view' of the scene, using the DoF Preview Button to emulate the final result.
I put a flash in a appropriate location (reasonably close to the mushroom, at a 45º angle from the camera), connected with an E-TTL cord and with a diffuser (I use Lumiquest Pro Max System). Using Av, the flash will behave like a fill flash (in M, it would have been the main source of light, with a completely different result), and with the difuser, the light will be soft enough to NOT produce harsh and unnatural light but will fill the darker parts of the image, resulting in a very pleasing image.
Finally, I take several shots, changing aperture, recomposing, doing exposure compensation, reducing or increasing flash power (FEC), repositioning the flash... until I have a shot I like.
Recently I've been trying to use two 580EX flashes to illuminate my mushrooms, but I still don't master that technique and I guess I'll be strugling with ratios for some time.
Regarding your second attempt, I find the first shot with a poor composition - you decentered the mushroom, but the base of the stipe is too close to the margin of the picture, the mushroom is not straight and there's an unappealing void in the left half of the image. Shooting mushrooms is not quite like taking a portrait of a person, where you can use eyes direction to 'fill' that void (or, better said, the void allow the look to breathe), because mushrooms don't have eyes. From my experience, I believe only two tipes of mushroom photos work well: close portraits or environmental shots (where the mushrooms take a smaller role in the picture, that shows more of the surroundings). In other words, I'd prefer a tighter vertical composition with a straightened mushroom,  The second picture results better IMO, because the fallen branch (or root?) balances the composition.
Right now I don't have images to post, but next week I'll have access to my archives and I'll post some pictures to ilustrate my words.
By the way, if you ever get interested in identifying mushrooms, here are some tips to your species: #1 and #2 may be the same species and I suspect they can be Cortinarius sp. #3 is not a mushroom: it's a Myxomicete called Lycogala epidendron (http://en.wikipedia.org/wiki/Lycogala_epidendrum). From your second post: I think the first species is, again, a Cortinarius (maybe the same species as before) and the second picture is of Hydnum rufescens.
Keep taking pictures and keep posting!
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