Well A Proper Tuning Is Needed To Make Engine Run 100% But If Its Running Now All Good...Don't Mess Around Much....Alto Is No Match For 4EFE As Power Difference Is Almost Double....!! Weight Of Cars Matters..Anyways
On Petrol It Should Accelerate Fast Compared To CNG But Topend Will Remain Same For Both....!!
You Can Attain Enough Speed To Meet Your Needs....!! Just Check For Plugs And Wires And Make Sure They Are Working All Good....!! Wiring As You Said Is Already Checked...I Know The Major Wiring Is All Good But Still Its Not 100%....Most of The Sensors Are Still Missing As They Just Wire Engine To Start Car....!!But If U Fell Ok..DOn't Mess Around....!!
Regards