It is very possible you could have an air pocket trapped in the engine and that could be preventing the coolant from circulating.
To aid in burping the cooling system on a 3800 swapped Fiero, I first drill a 1/16" hole in the thermostat so air can more easily bleed past the thermostat. You don't want to drill any bigger of a hole than this because it can impact the operation of the thermostat if you do.
You said you were using a factory location mounted alternator, so I have to assume you are still using the factory 3800 alternator bracket that has both heater lines running thru it. If so, here is how you can try to fill the system.
1) With a completely cold engine and with it off, remove the upper most heater hose from the alternator bracket.
2) Open the air bleed valve on the t-stat housing (if using the stock 3800 t-stat housing).
3) Remove the radiator cap and place a drip pan under that side of the radiator.
4) Install a funnel into the alternator bracket's heater hose fitting and slowly begin to fill with the proper anti-freeze and water mix.
5) As soon as antifreeze starts to overflow at the radiator, reinstall the radiator fill cap.
6) Top off the radiator overflow tank to the ADD mark at this point.
7) Continue filling coolant into the alt bracket until it either won't take any more or coolant starts coming out of the bleed screw on the t-stat housing. Close the t-stat housing bleed screw.
8) Top off the coolant level at the alt bracket fitting and then reinstall the heater hose.
9) Start and run the engine until it builds some heat and the t-stat housing starts to get warm. Once it gets warm, crack open the bleeder screw to see if any air or liquid comes out. Leave the screw open if only air comes out, but close it if liquid comes out.
10) Continue to let the engine warm up while periodically checking the bleed screw as instructed in step 9. Do not let engine coolant temperature exceed 230 deg F as indicated in a data scan. DO NOT rely on the Fiero temp gauge for an accurate temp reading. If the engine temp reaches 230 deg F, the radiator fan should be running before it gets to this point and pulling hot air out of the radiator. If it is not pulling hot air out of the radiator and the coolant temp continues to rise, then the coolant is NOT circulating thru the engine properly - shut off the engine to prevent overheating if you get to this point.
If you have your radiator fan wired up under PCM control and the PCM tune is set up properly, the radiator fan should turn on and off periodically as the engine sits there and idles at normal operating temp - and this should maintain a fairly steady engine coolant temp.
After you have verified proper engine operation (and it is not overheating), top off the coolant in the radiator overflow to the "FULL" mark. Check this level with a hot engine over the next 2 days of normal driving to make sure it stays topped off. After you check the level these 2 subsequent times, it should not begin to fall (disappear) from the overflow. Fluid level should remain constant based on engine temp (overflow tank level will vary depending on engine coolant temp, but it should never go empty and it should never go over the FULL mark with a fully warmed up engine).
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[This message has been edited by Darth Fiero (edited 06-26-2015).]