I think you have two options. The first is to order a long, undrilled, gunsmith's pic-rail, these are available from Brownells, but there might be unintended consequences. Specifically it might prove inconvenient for loading a rotary magazine if you don't have a "C" model, and because its been a long time since I shot a 99, I don't remember the angle of ejection, and can't definitely say it would cause ejection problems, but its something to check out before committing yourself to that option.
The other option is to have a gunsmith design and build you a custom quarter-rib, inletted for the rings of your choice. Rather than drilling holes in the barrel, a better mounting solution is to have it designed with a tail at the rear of the mount that can be screwed to the front of the receiver and either silver soldered or epoxy the front of the mount to the barrel. Permanent mounts, don't sake loose. I had a custom quarter rib built for a Ruger #1 that was inexpensive for custom work, but IIRC, the nicely made quarter rib for my Brno 602 was pricey. You don't need one that is stylishly scalloped, which would look out of place on a 99, and it should extend flat out from the receiver without any rise.