Magdalen, I have followed your links, thank you for providing them. I have read those studies before - some of them available in full and they really need to be read in full in order to determine how relevant they are and what the methodology is.
To begin; as is said so much on this subject, autism is not one thing. That is why it is considered a spectrum; ASD. And that is very very important. The children on the spectrum are all individuals and they all have their own bodies, history, genes, predispositions and lives. Some children become autistic because they are exposed to rubella in utero, some because they have been exposed to a virus at a key time in their development. There is more than one cause of autism and there is more than one autism.
Dr Wakefield et al were concerned with children who presented with regressive autism and particular intestinal symptoms and in which both of these issues manifested after exposure to a triple viral vaccine. Their work (the Lancet paper and many others) is relevant to this particular population; a subgroup of autistic children and a small subgroup of the many children who were exposed to the triple viral vaccine.
In order to attempt to re-produce Dr Wakefield et al's work, a scientist needs to examine the same population. If a different population is studied, no light will be shed on what is or is not happening in the population identified and examined by Wakefield et al. This is basic science.
Of course, one can google and come up with several studies which show a lack of association between children with ASD who received MMR and measles antibodies/infection. And of course one can draw the conclusion that those studies did not detect measles in the children they examined. In the populations they examined. To then draw the conclusion that Wakefield et al were wrong/fraudulent/lying is a not only utterly unscientific but also rather bizarre. That isn't how science is done - particularly when dealing with rare and novel conditions about which we have very little information. Especially when examining developing children.
So, now let's come to the studies by which you set so much store and seem to think show no link between MMR and autism in the population studied by Wakefield et al. (They do no such thing BTW. They do not scientifically allow one to make anything like such a conclusion. Again science doesn't work like that. The only way to test Wakefield's theory is to test the same population).
I don't have much time just now so I will take just one example; that of the (infamous) Hornig study.
You link to the full version of this study but have you read it carefully?
Firstly we can note two things; one, that the study involved examining children using colonoscopy. (Something Wakefield et al were presented as being equivalent to Nazi medical experimenters for doing. And they were doing it for clinical purposes whereas Hornig et al are doing research with the objective of exonerating a vaccine 
)
Secondly, the Hornig study uses Dr O'Leary's lab and notes that;
Results were consistent across the three laboratory sites. and All laboratories correctly identified all positive controls using pre-established criteria for positivity (positive results in at least two of three wells with at least one of the primer pairs for F and one of the primer pairs for H). All laboratories correctly identified all negative controls.
Mmm so they use the O'Leary lab which was supposedly contaminated with crappy control methodology. Or at least is was when they found measles in autistic children. It seems that when Dr O'Leary doesn't find measles in autistic children that is good and consistent across the three laboratory sites.
Now, onto the results. Well they did detect measles virus in two subjects;
Analyses in all three laboratories found two ileal biopsy samples with MV F gene and H gene RNA: one from a boy in the AUT/GI group, the other from a boy in the control group.
(Remember that the control group was not made up of healthy children but children with GI disturbances alone .)
And then the real problem which comes with the selection of the study subjects themselves. 25 children with autism and GI disturbaces were studied but out of the 25, only 5 of them developed symptoms after MMR vaccination. In other words, only 5 belonged to the same subgroup as that studied by Wakefield et al. And of those 5, one child had persistent measles infection in his intestine.
Here is a copy of the press release from Thoughtful House in response to the study;
Autism Researchers Comment on New Study and Welcome the Affirmation of Previous Measles Findings
A study published yesterday in the Public Library of Science One (PLOS1), an on-line journal, failed to find evidence of measles virus in the intestinal tissue of 24 children with autistic regression and gastrointestinal symptoms. The findings contrast with those published in 2002 in which researchers from Ireland and the UK found measles in 75 of 91 biopsies from autistic children with GI inflammation, and in only 5 of 70 samples from non-autistic children1. The children with autism in the 2002 study developed gastrointestinal symptoms and autistic regression after the MMR vaccine.
In the study published yesterday, conducted by three independent laboratories, only 5 of the 25 children developed these symptoms after the MMR vaccine and therefore, only these five are comparable to the 2002 study. This new study confirmed that results from the laboratory of Professor John O?Leary (one of the collaborators on the new study, and senior author of the 2002 study) were correct, and identical to the results obtained by the laboratories of the Centers for Disease Control and Prevention (CDC) and Dr. Ian Lipkin of Columbia University.
In that this new study affirms the reliability of Professor O?Leary?s laboratory and therefore of his previous findings, a major impact upon the current hearings in vaccine court is likely, wherein the government?s defense relies largely on the claim that Professor O?Leary?s finding of measles in the intestinal biopsy of Michelle Cedillo (a child with severe autism and epilepsy) was unreliable. The historical reliability of the measles assay used in Professor O?Leary?s laboratory is now confirmed.
The authors of the PLOS1 study make the erroneous claim that epidemiological studies have not supported an MMR-autism link, when in fact the CDC?s own study published in 2004 shows a significant association between autism and younger age at the time of MMR vaccination 2.
We are pleased to see that this new study provides further confirmation that children with autism suffer from gastrointestinal problems that deserve to be addressed as a priority. Dr. Andrew Wakefield, Executive Director of Thoughtful House Center for Children, whose work has focused on intestinal disease, and on the possible role of MMR vaccine in regressive autism in children with GI symptoms, welcomed these new findings. Dr. Wakefield was a co-author of the 2002 paper that, unlike yesterday?s study, examined children in the majority of whom there was a clear temporal link between MMR exposure and regression. Dr. Wakefield comments, ?The search for the ?footprints? of measles virus in the intestine is merited, based upon the previous findings and the intestinal disease that is commonly found in these children. This new study rules out only one possibility ? that the measles virus must remain for the long term in the intestine. We need to consider that the MMR vaccine can cause autism as a hit-and-run injury, but not necessarily leave the measles virus behind.?
While we welcome this study as a piece in the ever-growing body of evidence that illuminates the complexity of autism and the possible factors that cause it, it is clear that yesterday?s study does not establish that the MMR vaccine is not associated with autism. This work examines one small part of a very complex equation, and in fact by affirming Professor O?Leary?s laboratory and assay methods, it inadvertently endorses the validity of his 2002 findings of vaccine-strain measles virus in the gut tissue of a group of children with autism.
So hardly so cut and dried as "there is no link".