To drill the pump, you remove the steel line going to pump, then you remove the threaded collar that the steel line went into. This is the part you need to drill over sized.
Now how many steps really just depends on you and your system you built, like what size ID ram VS what size chrome rod used in ram, how big of line's and how well you struck the pump veins when you drilled them.
I went two steps over with my Jeep when I did it, I used a 2x8 ram, with a 1 1/8" chrome rod, -6 lines and hit the centers of my ports on my box.
When I upgraded to full hydro I couldn't really tell the difference between the two once I was done.
The box, well without Pics ( which I have none taken when I did mine ) its hard to pin point the veins that need to be drilled but they are there on the bottom of the box.
I left mine in the Jeep with the Res. full of fluid, after punching threw the fluid was draining out, not fast but enough to wash any metal shavings away.
Then onto to tapping it, yes you needed two taps, they are 3/8" pipe taps. One will need to be cut in half so the thread will bottom inside the box. start tapping the holes with the uncut tap, finish or bottom them out with the other tap, the cut in half one.
The last thing I did was clean the hole, even with fluid draining at a good rate out both hole some shaving stayed in the thread section and got into the ports.
I took a strong magnet, stuck it to a small screw driver and used that to fish out any metal. That worked very well and after about 20 min or so I was satisfied that I got it all, which I did.
1993 YJ 4.0 60 Front, Rear steer 60, bolth spooled, 5.38's, 700r/241 39.5 iroks and beating it like it owes me money.
And on the 8th day, God created the 14 bolt....