I have a 99 Accord VTEC as well. I have the F23A1 Engine. I had a similar issue about 2 years ago. The timing belt was about to snap and I was desperate and I took it to a Meineke near my job. They returned it to me, missing a bunch of bolts to the alternator, power steering pump, etc. I had squealing serpentine belts. I took it back and yelled, they fixed it. The vibration was minimal to me.
Months later the vibration got way worse! So bad I couldn’t accelerate without thinking the engine would take off without the car.
I examined the engine mounts. They were all shot and shredded. I imagine the mounts were original (16-17 years old at the time), and when they accessed the timing belt cover, they had to remove a mount. When they did that I assume they did not prop the engine. The additional weight on already old mounts, trashed them all.
I would inspect the engine/transmission mounts.
My advice also, is to not skimp on the mounts if they need to be replaced. OEM Mounts have rubber, most aftermarket mounts are neoprene or something stiff. If anything, and the A/T mount underneath the Air Intake is shot, get an OEM mount for that. It has a vacuum hose, that inflates the mount while idling. Aftermarket replacements just seal that line, and the mount won’t function as intended.
Sorry for the long response. But I’d check the Engine and A/T Mounts.