I work on various 5 needle pines both US-native and not, including limber. These needle issues you see are no big deal (esp in light of you saying new growth looks good, and it LGTM too) and so I wouldn't troubleshoot needle issues too much this year. You can and should clean out old busted needles as you see them shed or go brown.
There isn't much out there that threatens a limber pine as long as it's in full sun and you're watering thoroughly when you do water (i.e. strong flush) and are making sure to water infrequently (i.e let top soil dry out a bit before rewatering). Anything that does pop up this year, before you've started the soil transition and root edits, is going to ultimately be solved by that soil transition and those root edits.
For this case, almost (see borer note) all pathological roads lead to (in stages) bare rooting into pumice anyway. If you fear borers or adelgids during weak periods, you could treat with imidacloprid (example product: bioadvanced "tree & shrub") a couple times a year, notably in the spring as its waking up and pushing.