It's pretty common in fiction these days to have a romance plot and a mystery plot running simultaneously. It's probably worth your while to study what cues authors give to help the reader stay oriented. Beta readers are good, too-- if you're going that route, ask them to tell you if they start getting confused, and if so, where. (Second-hand information: beta readers are more useful for identifying problems than for suggesting solutions.)

You might need to work on plausibility if you're adding threads, especially if your main characters are deeply involved in all of them. Does your philosophical problem have something to do with the AI? With the romance?

Rowling's A Casual Vacancy (recently released, not fantasy, depressing) does an impressive job of tracking the consequences of many goals and consequences through a large cast of characters.

I think time could go either way in the past. I assume you're talking about flashbacks where time goes forward in each flashback, and your concern is what order to put the flashbacks in. Off the top of my head, I think the question is what you're trying to build suspense about-- is it revealing a root cause for the whole situation? Flashbacks in reverse order. Or is it revealing the whole sequence of your story? Flashbacks in forward order.

I recommend research on the flashbacks problem. I assume someone (among all the books and discussion boards about how to write) has addressed it, but I've never seen it done. Also, how are flashbacks handled in your favorite books with flashbacks? Reading like a reader isn't the same are reading like a writer.