What to keep in mind when installing a 1998 Camry Solara engine in a 1998 Camry LE?

When the engine blew in our 1998 camry due to vanishing oil (we had just checked the oil the night before!), We called Japan auto parts which feature 50,000km engines but they did not have an exact match but said that a camry solara engine was close to the same so we installed it 5 months ago. My question is this, is the camry LE motherboard compatible with the replacement solara engine or should we have asked them to send us the solara motherboard with it? They (japan auto parts) did not say anything about needing the solara motherboard but we are having a few problems with our car and just wanted to know. Symptoms are:

Idling right after starting car goes up and down repeatedly for about 4 seconds then idles normally for aprox. 1 minute then again up and down for 4 seconds. It does this for about 5 minutes then its ok. Every now and then, it develops a vibration at red lights, the kind that bothers your ears, if that makes any sense! And every now and then, you get a whif of gas in your face and loss of acceleration especially after second shift (its an automatic not standard). Its also hard enough on gas for an engine with only 50-55,000km at time of purchase.

constant smell of coolant but amount in reservoir does not change, car does not overheat, we have plenty of heat from vents, there is no coolant in oil, leaks cannot be found even in white snow (again, amount in reservoir stays the same, we checked the water pump, heater core for blockages and nothing! Just in case however, we bought a new rad, new thermostat, new hoses and clamps, new alternator, new battery, new spark plugs and even had it hooked up to 2 different code readers and the only codes that came up was a bad EGR and bad VSV which we fixed so we are lost! Thanks for anyone's help!