Chevy 3100 V6 Timing Problem Help!!!!!?

Okay here is my problem I have a 96 oldsmoblie with the 3100 v6 in it and im trying to regain time back. the book says have the cam and crank gear aligned up and down and cylinder # 1 will be TDC and cyl. # 4 will be firing.. heres my problem done that i have aligned them correctly but the only thing is that cyl. # 1 is not TDC its BDC so i have spon the crank 360 still the same the only way cyl 1 is TDC is when the crank is spon 140 degrees to the right. that is the only way i can get cyl to TDC. but when having the chain on with the crank at 140 degrees out and the cam down center i can get the car to run rough i think i have to spin the cam over a couple to degrees to have it in time with out haveing to swap plug wire to acheve center timing.. any word on help for me please...