I'll do exactly their procedure.
That's fine, but I would make one change. Unless you pre-set your ignition base timing accurately as they did, I would plan on checking timing as soon as the engine is running and stable at elevated rpm to avoid other damage during break-in.
Question, I've driven about 5,000 miles like this with three oil changes in between. With the metal dust that came out, how worried am I that my bearings and journals will get scored as well???
They already are. The question is not if, but how much. With good filtering to keep larger particles out when it happened, and more filtering to keep new dislodged floaters out of the system, you may well be "okay". In the crankcase, particles like yours tend to stick in and on the metal surface, only to dislodge later. In other words, you will have issues to deal with one day during a rebuild (crank scoring, and accelerated wear in various places), but the engine may go quite a long time if the existing damage is not too severe. If signs are present or appear later that indicate excessive accumulated damage, then it's time to think about repair or replacement of parts or the whole engine. Excessive blow-by, low oil pressure, noise, etc. are common signs of that damage.
Besides your good move of multiple oil changes, common tricks are the magnets, and better filtration such as non-bypass filters, or oil filter inlet screens and dual-filter adapters. Dual filters permit the flow to reduce through each filter, to reduce the likelihood or degree of the filter's internal bypass valve opening, which allows unfiltered oil to bypass directly to the engine internals. Most racing filters do not use bypass valves for obvious reasons, but they are expensive.