You stated that ports 3 and 42 were configured on the Catalyst switch, but then provided configurations for ports 46 and 48. The configuration you posted for port 46 should be applied to port 3 that connects to the EX2200. Your router's connection is unchanged, so hopefully we can assume that configuration is fine.
Now, on the EX2200, the following lines of code would be appropriate to do the following:
ge-0/0/0 - trunk allowing the same vlans as defined above on port 46
ge-0/0/6 - access port on VLAN80
set vlans vlan80 vlan-id 80
set vlans vlan82 vlan-id 82
set vlans vlan83 vlan-id 83
set vlans vlan93 vlan-id 93
set vlans vlan289 vlan-id 289
set interfaces ge-0/0/0 description uplink-to-catalyst
set interfaces ge-0/0/0 unit 0 family ethernet-switching port-mode trunk
set interfaces ge-0/0/0 unit 0 family ethernet-switching vlan members vlan80
set interfaces ge-0/0/0 unit 0 family ethernet-switching vlan members vlan82
set interfaces ge-0/0/0 unit 0 family ethernet-switching vlan members vlan83
set interfaces ge-0/0/0 unit 0 family ethernet-switching vlan members vlan93
set interfaces ge-0/0/0 unit 0 family ethernet-switching vlan members vlan289
set interfaces ge-0/0/6 unit 0 family ethernet-switching port-mode access
set interfaces ge-0/0/6 unit 0 family ethernet-switching vlan members vlan80
Some other suggestions for you:
1) Turn on LLDP on your switch so you can do a show lldp neighbors and see where your connections go.
2) Don't use RSTP for spanning tree on the juniper switch, it doesn't play nice with Cisco that well, use VSTP instead. If you end up with a ton of vlans, you might even need to use MSTP.
3) Turn off chassis alarm for the management ethernet if you're not using it.
On the EX2200:
delete protocols rstp
set protocols vstp vlan all bridge-priority 4k
set protocols lldp interface all
set chassis alarm management-ethernet link-down ignore
On the Catalyst (if it supports it)
lldp run
First let me state that I'm over simplifying this a lot and I'm also making assumptions we are talking about Cisco switches and not necessarily some of the routers or advanced ways of handling traffic.
My Cisco knowledge tends to blend with others like Juniper and Extreme, but...
"a tagged port is used to allow a host to be seen from different VLANs" - no/not necessarily, depends on lots of factors.
Trunk ports are typically used in switch to switch or switch to router links or between ports that require multiple VLANs. They are used to transmit packets from multiple VLANs between gear usually and will add 802.1q tags to the traffic to differentiate between VLANs. By default a trunk port will pass traffic for all VLANs but you can set allowed VLANs to further lock it down.
"static" Access ports belong to a single VLAN and accept traffic only from that same VLAN.
Other vendors besides Cisco will let you tag "access ports", for instance Extreme doesn't even call them trunk/access, you start with an untagged port and tag it with multiple VLANs as necessary.
This pic might help since there are other ways to do things like a dynamic access port or voice port nowadays:
Hope that helps.
REFERENCES: http://www.cisco.com/en/US/docs/switches/lan/catalyst3550/software/release/12.1_19_ea1/configuration/guide/swvlan.pdf
Best Answer
So first, what is your native VLAN ? I'll identify it by ~native~.
You need to set the port 10 as on the vlan 1940
Now, will configure the port 24 to tag and manage packets for and from vlan 1940 as wanted :
Finally, to tag packet, you will need to configure 802.1Q protocol.
So now, your switch is configured to tag packet from vlan 1940 with the 802.1Q protocol.
EDIT
Everytime you need to add a VLAN to a trunked port, you'lle need to make the last step and add the
switchport trunk allowed vlan <num>