The problem there is actually defense. Adding Harper plus a bounce-back season from Herrera plus improvement from Kingery and Alfaro and high OBP from Crawford (who had an .800 OPS in his limited action after initial slump) could easily add you 10-12 offensive WAR. But if Hoskins is still in LF and Harper isn't that much better than Williams you might not improve much.
This game is a lot easier to play with Machado. Then I think they really can play Santana/Crawford at 3B as stated (with Santana and Hoskins splitting time at 1B). Kingery at 2B or heck, in AAA if they keep Hernandez (and the team's ego can allow it). A veteran OF to share LF with Hoskins and RF with Williams. Bench is Crawford/Quinn/OF/catcher.
What I think your complaint really highlights is why Harper isn't the right fit. He costs the draft picks, he's going to get more money if Boras has his way, and adding him leaves fewer obvious avenues to improve the team as things currently stand. Trading Santana, moving Hoskins to 1B and adding a second OF would be one way to do that, plus you could also sign a 3B, albeit with some risk. Playing Santana at 3B part-time and Williams at LF part-time would be incremental improvement if Williams produces (or you could play Herrera in LF and Quinn in CF, at least for a while).
My guess is they get Marwin Gonzalez. He can play the OF, he can play 3B and if they move on from Hernandez he can also play 2B if necessary (say, if Crawford gets hurt and Kingery's back at SS. Though obviously that won't matter if they have Machado).
I dunno about this because I think Manny will sign well before Harper. I still can't see them getting both but that would certainly end the shopping list!
I really do think Santana is more likely to play 3B then Franco. Franco is easier to trade (and may never be more valuable). And I don't think the positional flexibility thing is a cover, I think we'll still see a lot of it.