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There are some helpful resources on SupportNet that you can check out. Specifically, TechNote MG249665 might be really useful for you. It talks about using Hyperlynx SI in the EE flow.
I'll try to answer what I know though:
#1 - Check out TechNote MG249738. The properties that you need to set to get the IBIS model to come over into your LineSim schematic are SIM_MODEL_FILE and SIM_MODEL. Another thing to remember is the model directory needs to be setup in HyperLynx so it can load that model into the LineSim schematic, otherwise your net will appear to be missing the driver/receiver models.
#2 - This is really dependant on the process you have in place - companies do it may different ways. I'm not a front-end expert, so I'm probably not the best person to provide a recommendation, but I would think any of the options you mention below would be fine. From the HyperLynx side, you just need to map a directory to where these models reside so HyperLynx can find them.
#3 - Check out TechNote MG248623. You basically need to have the IBIS property on all your parts with the correct component name within the IBIS file. A .REF file gets created with IBIS model assignments if the IBIS models are defined in the central library and you've placed this IBIS property on the part.
#4 - It should be answered by #3 for the parts that have models. For things like discrete components such as resistors, capacitors, etc, HyperLynx will use the value defined in the part definition to make these value assignments. There's some good information in the Expedition User's Guide under "Import and Export Interfaces" > "Export to HyperLynx Power or Signal Integrity".