Only two bolts under the engine? Sounds like the instructions to change the oil on the Porsche Boxster: First, jack the engine...
Think of this an a good excuse to install new engine mounts, which will absorb more vibration, and reconfirm your propshaft alignment.
I'm sure a hand drill eventually will do it, and if the bolt isn't perfectly plumb it will still take load. Still...two years ago I had to have a discussion with a concrete wall and I bought a genuine impact drill, light commercial grade, because the wall wasn't near my home and my trusty Craftsman drill. Funny thing, having the right tool with the right power behind it made the job trivial. The average 1/4" or 3/8" home drill...let me guess, are they using three inch bolts or four? (sigh). I can't pretend to know if you'd even really need more than that, I'd just *suspect* the lagbolts should be as long as the real keel bolts, and I'd be shocked if those weren't over a foot long. Big hole for a home drill.
But there are drill guides for some drills, from some makers. Not very expensive, just not something that's always in stock.