2. Correct. The goal of the pre-processing step is to generate a Solr synonyms file which can be added to your index mapping.
3a. You could use all the words, but in general I would advise against it. Using all the words from Wikipedia or Google News would be similar to using a thesaurus which can add a lot of noise. For example, the word "cocoa" could mean chocolate, a city in Florida, or programming language. It is better to use a list of domain-specific keywords and phrases as a filter for which words are added to the Solr synonyms file. However if your corpus is Wikipedia, Google News, or something equally generic, then using all the words makes sense.
3b. It must be both query and index time. For example, the phrase "java developer" would have the mapping "java developer => cluster_15" in the synonyms file. In order for the search terms "java developer" to match cluster_15, "cluster_15" must be indexed in place of "java developer".
4. The different forms will most likely end up in the same cluster, but stemming would guarantee it.