Congratulations again @Mr.E! Your posts are really helpful, for those of us who still dream of being in your position! Hopefully movement from stage 3 to stage 4 will move quickly for you!
You appear to have already answered the issue of proof of residency question by stating that your lawyers obtained the Contagem do tempo to cover gaps in residency card periods: Wait time now counts toward 5 year residency? - #72 by Mr.E.
The main change since that post is that the law on nationality altered to include the waiting time from application" for residence to getting the first residence card, for those that get their card. The unknown is how AIMA will eventually calibrate the start date for GV card holders (date of application submission/payment, pre-approval date or biometrcs date?) once the law is in force this April!