Hi Everyone
As to @jreiss recommendation, I followed the provided CUPS guide and managed to connect the AEP Conduit to TTN V3 
One thing to notice, you need to use the default station config by multitech and not the station config settings you can download from TTN. This same config works for any channel plan when using CUPS as it will get the channel plan from the LNS.
if you overwrite it or don’t have it, you can grab it at the top of this article:
http://www.multitech.net/developer/software/lora/running-basic-station-on-conduit/
direct link for MTCDT station config
Few other tips:
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For TTN V3 you should use the ISRG Root X1 pem for Server Cert
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This guide shows you how the conduit setup screens look like: Connect Multitech Conduit with LoRa Basics™ Station | The Things Stack for LoRaWAN
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This guide shows you how to setup the GW and API Keys
Configuration and Update Server (CUPS) | The Things Stack for LoRaWAN
Good luck and hopefully you will now have a less frustration migration of Multitech Conduit to Basic Station than I did