When a buddy of mine put a new motor in his 01, he just zip tied the headers in the engine bay to hold somewhat close to where they would be, then bolted them up when he installed the motor, now is deff the time for lts though, while you already have the motor out.
I just removed my engine/transmission as one piece with the longtubes on, and installed it the same way.
I dont know what headers you have, but if you have the BBK longtubes, youll need to install the transmission before the pass side header. Do this with the engine out of the car to make it easier.
Jack up the back of the car pretty high, and use a load leveler to tilt the motor/transmission. It helps to have a friend work the hoist while you position the motor for the last few inches. I had to get my GF to lower the motor while I pryed between the motor and k-member to get it to clear. Also had to push on the motor while she lowered it to get the motor mounts in place.
Your milage may vary, but you will have to finaggle it some. The longtubes might try to land on the k-member, so watch that, and adjust as necessary.