First, let's be clear, I am not a gunsmith.
I use Weaver 2 pc bases entirely, on Mausers. My low budget home made methods are crude but work. Get a piece of 1" cold rolled or similar, 6 to 12" long, drill a dead true hole, 1/4" or so thru the long axis. This is your "peep sight". Attach your scope rings and bases, clamp the barreled action securely in a vise or vee blocks. Align the barrel bore, you're looking thru it, at a distant easily discernible object, put the "peep sight" with the bases and rings attached atop the action, adjust bases and rings as necessary so that the peep sight is aligned with the same "target'' as the barrel. Clamp in place, rechecking alignment, mark the base locations with a needle point scribe or your preferred method. Then apply an adhesive to the bases and the action, reassemble, recheck alignment after clamping firmly and allow time for adhesive to work. Remove rings and peep sight assembly, carefully transfer punch your receiver thru the base holes, remove the bases, spot, drill and tap each hole from the same setup on the drill press table. When done, your bases will be aligned to the boreline, which is more than you can say for some factory jobs where you don't have enough scope adjustment travel to compensate for mis-aligned holes.
Depth: It is much handier to un-barrel your action for drilling and tapping...but if you want to do it with bbl on don't be afraid to run the tap drill into the barrel threads a little, you will hear and feel the transition, be very cautious, this is where drills are shattered, I prefer to hand rotate the drill the last 50 thou or so.
The most important thing is to calculate the front to rear hole location on the front receiver bridge. Avoid ending up with a hole straddling the locking lug recess and the locking lug abutment. Front hole should be a through hole, rear hole can be a blind hole, you can measure receiver thickness at that point with calipers. If you buy new bases, you can use the screws supplied to calculate depth, remembering to go a little deeper for your bottom tap. I strongly suggest all three taps, start, plug and bottom. Last word, most modern scopes have very short main tubes for the rings on the long '98 action. If you go that route, the front base needs to be an "extension base" or an extension ring, think ahead.