So I currently have 5 Vlans setup on a CCR1036 with most of the ports on the router configured as access ports for one of the vlans. I also have 1 port which has all the vlans tagged on it to another switch working with no issue.

My confusion is I want to have another trunk port that only carries 4 of the 5 vlans and I cant seem to figure out how to do this. Currently all my vlans are setup on a bridge interface BRTRUNK. Is it possible to have multiple trunks from one router each containing multiple overlapping vlans but not the exact same vlans?

Yes totally possible. I can probably help you but need to see it in Winbox to wrap my head around it. So confirming you have all your VLANS on a single ethernet interface (Say port 2 for example)? Then you should be able to create a bridge and in that bridge have all the VLANS you want and then say ethernet port 5..... Does a setup like this work?

Also why do you need two different trunk ports on your router that would carry some of the same VLANS as each other?