A potential client has a slow ecommerce site using Joomla/Virtuecart which takes 6-10 seconds for any page to load. I've seen faster solutions and would like to transfer the 4,000+ products with little hassle to a speedier, more full-featured open-source solution.
Re 1.: Depends strongly on the data structure both on the sending and the receiving end. Either way, be prepared for some work and trouble.
As for 2. I can't make a shop system recommendation but I would say, try optimizing what you have first. Joomla is not a pinnacle of code quality and performance - I can't say anything about Virtuecart as I don't know it - but there must be some caching solutions around that are definitely worth trying out first. Also, check what other Virtuecart users have done. It might be that much can be achieved doing comparably little tweaking.
And second, it's always the question what is causing the slowness. It could very well be a hosting environment equipped with too few resources, or shared with too many other customers. Before recommending switching to a different solution, I would first e.g. make a local copy of the system and see how it behaves on a normal machine. Maybe even try to install on a different webspace, if it's not too much hassle.
In answer to number 1, schema migrations are a very delicate process and should always be treated with care. Do several test runs before doing anything permanent, live, or destructive. Look for edge cases, funny encodings, etc.
For number 2... I haven't worked with a whole lot, but Zen Cart and Magento come to mind off the top of my head.