Alright, I just dealt with this last week...
I tried to smog a custom fuel cell in my 94 YJ, and the smog tech basically laughed in my face. You are going to need to make an appointment with the smog referee. Since the tank is not (I'm assuming) SAE approved, etc, the vehicle will not pass no matter what your filler neck looks like. Just make sure to hook up the breather hose (like the two that were on the stock tank) to the charcoal canister lines. They should still be there unless you ripped them out. If the referee doesn't like it, then do what I had to do... swap the stock one back in to pass emmisions

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I talked to the guy that was doing the smog and asked him if he would "notice" if I had the stock tank hooked up to the stock filler (no sending unit) and all bolted in so it looked normal, with the fuel cell in. He said that as long as the fuel cell is hidden, like under a blanket or some gear, that he would have paid no attention. All they do is pull the cap and put it on some pressure test thing. The rest is a visual inspection.
Hope that helps, good luck.