First you may want to make sure they're actually expressed -
SHMT and/or ACAT mutations: Consider addressing these first if you or your child have any of the following test results: elevated iron on a UEE test, Short Chain Fatty Acid (SCFA) imbalances on a CSA test, suberic, beta hydroxyl methylglutaric acid, or other ketone and fatty acid metabolites imbalances on a MAP or OAT test; or if there are severe gut issues or muscle weakness (which can be related to aluminum retention)
If you have SHMT/ACAT, treating those first, then working on the gut will help with the gut issues. If you just worked on the gut without treating SHMT/ACAT, it may not be successful, or as successful.
I can't find where Yasko says specifically how long to stay on the ACAT/SHMT supps, but it sounds like to me that once your gut is in good shape, you could discontinue.
The MTHFRsupport people just mention working on the gut if you have SHMT/ACAT and not doing the other supplementation.
Anyway, I think this would be a good question to ask on the Yasko forum. The moms over there have a lot of experience and are happy to answer questions
http://www.ch3nutrigenomics.com/phpBB3/welcome.html
However, if you have trouble with kidney stones, I believe I would stay on bile salts and a low oxalate diet permanently to help prevent them.