What should I set the timing at and should I leave the spout plug in or use it?

Hello, the base timing for this engine is 10 degrees before top dead center (BTDC), you set the base timing with the SPOUT connector out and then reconnect it after you have the timing set, if you leave it out you won't get any timing advance at higher rpm like it's supposed to. I'll post the base timing instructions for you. The last diagram is the crankshaft pulley and the timing marks on it, with the spout unplugged set this to 10 BTDC, and then plug the spout back in, and you should see the engine computer advance the timing at higher rpms. It has been a long time since I've set any timing like this. Hope it runs great for you. Sounds like you did a lot of work on it.

Yes, you can jump the spout connector, it's just closing that circuit, as for the tuned ECM, is this something you just bought already set up? Most tuner ECMs come with software that you can change the fuel mapping strategy; you can set it for more torque or change the injector pulse width. They usually come as a kit, well the ones I've looked at before. This is an OBD1 system, so you'll need an adapter for a scan tool, but below is a list of the data pids that should be available.
But maybe getting in touch with the company that programmed the ECM can tell you what they do for a set up. Where did you get the tuned ECM from?

With the cold air intake do you still have the intake air temperature sensor in the mix, or was that taken out with the new ECM?

I gotcha. If you deleted the EGR system I assume you don't have strict emissions in your state. They're terrible here. Its every year and its expensive, I'm going to check out the company you got your tuner ECM from, I just want to see if they offer any PC software programs for making changes.