I know it has been covered and struggling to find in via search. Have missed the window a couple times on timing arbitration eligible players to long term deals. Could someone share a solid explanation on timings within seasons to make these decisions?

Sign him to a long-term deall before his third arbitration season. He'll have 5 years ML experience. If you wait until after you've arb'ed 3 times, the player will likely not sign.

You can sign your arb eligible guys in cycles 4-9 of the season (days 2 and 3 of the season in real life, after your team budget is set in cycle 3 and up through the last cycle of arb negotiating in cycle 9). Go to the arb report page (GM tab -> Contracts -> Arbitration report) and click on the "Negotiate LT" link and sign whatever long term deal you'd like.