dude after doing an engine swap after having a big end go there are a f load of hoses you wont even realise are vaccume lines, two of which are hard up against the fire wall and there is no way in hell you can do them without pulling the motor out
i wouldnt mind hearing the issue your having cause it sounded like at first the problem mine had which was the alternator had gone so the car would get absolutly no power and ran rough as hell. but if its still starting then i guess that's not the issue other wise your battery would be dead by now