I don't think you're going to find really long bolts like this at the hardware store, and no, that long lower bolt is not available from Yamaha anymore. It's kinda special, having a different head style than the others (domed). Occasionally, I'll pick up misc. parts assortments off eBay, usually from the seller mistermonkeyclaw. One of the items I look for them to include is that long lower engine bolt. Here's one that has it. It's right at the bottom of the pic .....
https://www.ebay.com/itm/232933779536?hash=item363bef6850:g:6JgAAOSwDyxbmQhd
I also count the number of acorn nuts included. As you're probably aware, most of the ones on this bike are rather specially sized, having smaller heads and/or domes than a standard replacement does. And while most are still available from Yamaha, they're not cheap ($3 to $5 each). So, if there's like 8 or 10 of them included, I figure that pretty much covers the cost of the purchase.