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
Best Answer
Probably you already know this, but I'm pointing it out anyway.
As Radius said, you can configure a single port in trunk mode; but this means tagged 802.1q Ethernet frames will be sent to that port, so you will need to connect to it something which can succesfully decode and detag them (like a trunk port on another switch, or a trunk port on a ESX host).
You will not be able to simply connect a computer's NIC to that port and have it connect succesfully to any one of those three VLANs. That would require 802.1q support on the computer itself.