Hi
Well it is a practice done often, but do not expect to get the same rankings as you had with the micro-domain, you will see some drops. Some will gain their rankings back and others will need SEO push. The time it takes depends on many factors such as domain authority, site freshness etc..
Whenever i go and merge domains or incorporate them, i try to find the best user-friendly category architecture. First it should make sense to the user (how everything is lined up) and than to google.
IMO, if all the redirections are done correctly, the only problem that you might have is with the pre-existing categories. I would double and triple check all URLs, run extensive crawls on the site with Moz Crawl (limited no# of URLS though.. ) DeepCrawl, Screaming Frog etc. and look into the URLs. Its amazing how one program cant find some URLs and others do.. You will want to avoid duplicate content issues
Of course i don't even mention how closely you need to monitor everything.. I would do a list of the most important URLs to be transferred, and closely monitor them. Also i always suggest to go with very minimal content changes(also meta changes to minimal).. keeping it as close as to original and only then, after everything is good and healthy, i would go and start making improvements on the content..
I know how much time consuming robotic job it is so good luck
P.S.: Also it's a good and common paractice to go ahead and contact site owners for the relevant good and natural backlinks that you have gathered over time..