It's not too late, but you don't want to delay more than you need to get the points together. Award availability is always limited, so there's a chance the lowest mileage seats will no longer be available when you're ready to book and you'll have to settle for higher mileage award seats or redeeming points through the Chase travel portal.
I'm not a fan of direct debit because in most cases you're not earning anything on it. You mentioned that you're earning 3% back if you make 15 transactions of $10 or more. That's something. But with my wallet of cards that offer bonuses on a broad range of categories, I'm almost always earning 3x or more on my spend. And if you're working on an new card MSR, the return is even higher. Take for example the CIP, you'll get a minimum of $850 worth of points back on $5,095 spend -- that's at least a
16.6% return, more if you're hitting 3x bonus categories during your MSR period.
As I said, it looks like you can get 2 RT flights for DMS<>NRT for as little as 140k miles on UA, which can be transferred from 140k UR points. If you do 2 CIPs, that's a 80k UR signup bonus for you, 20k UR referral bonus for you when you refer DH, another 80k UR signup bonus for DH's card, and at least 10k UR from the combined $5k+$5k MSR =
190k UR points. 140k UR for flights would leave you with 50k UR. You could stop there. This is your plan, your finances, so where you start and stop is your choice. But if you want to pay for hotels with points or upgrade your hotel options, book activities, offset the cost of JR Passes or Tokyo
Disneyland tickets, start saving for your next adventure, you can do all of this with more points. Because you're starting with a clean slate, my notepad math tells me you can easily earn
342k more UR points by signing up for at least 3 of Chase's other UR-earning cards, meeting the minimum spend on them for the signup bonuses, then referring DH for the same cards, meeting the spend and earning the bonuses too. 342k UR + 50k UR leftover from your CIP = 392k UR, which if redeemed through the CSR (one of the cards you'd be signing up for) with its 50% bonus would be worth up to $5,880 in travel.
Depending on how many points you need, you may not be able to cover your trip 100% but...covering half the cost is better than nothing, right?
In this instance (assuming 190,000 points) - you could transfer them to United and pay for those flights (which I think cost > $3,000). You could also use them through Chase's travel portal and they're worth almost $2,400 (or if you later get a CSR card they'd be worth over $2,800). 
I doubt it's an actual acronym, but Math Is Your Friend will tell you to add up the 3% you're currently getting on the checking account between now and your trip, then compare it to what you could get with the credit card bonuses. 
