Your engine is made up of many different types of castings, all which have different porous surfaces. Depending on what cleaner you used, and any kind of pre-wipe, those are retained in those pores. Your problems will only get worse once the engine is run and heat cycled. Also, paints themselves have reducers that must flash off. New "low VOC" paints are horribly slow flash times to meet EPA laws. Adding multiple coats just makes it worse.
If afraid the only option is to strip the engine, clean, bake and then repaint. Make sure you paint at above 70-degrees and then bake after 3 coats. Leave at elevated temp for about 48hours.