I just did these mounts a couple weeks ago for the same reason (cracked manifold). Driver's side motor mount was pretty far gone, after taking it out the sleeve that the mount pins go through would just flop around in there. Passenger side looked alright, but replaced it anyway and saved it in case the new anchor mounts crap out. The transmission mount was pretty worn out as well.
To jack up the engine, after loosening all the motor mount bolts I put a 3x3 block of wood under the oil pan (the flat part near the drain plug) and jacked up the pan. It is trail and error as for how much to lift it; at some point the pins will slip out of the mounts...it took me more lifting than I expected b/c at first all that gets lifted is the suspension from the engine's weight being removed.
Anyways, after removing the pins you can easily take the old mounts out. Put the new ones in and get the bolts/nuts started, but don't snug them; you might need a little bit of wiggle room to get the new pins in. For me the drivers side pin went in straight away but it took me a while to get the passenger side pin in. I used a prybar between the mount and motor to get the alignment close, but it was still tight. Once I had it lined up as close as I thought I could get it, I lubed the pin with grease and tapped it in with a mallet. Ideally you can get it without the mallet though. If you have trouble with alignment, loosening the bolts on the transmission mount might help.
As for the transmission mount, if you've got a bad motor mount, or probably with just 150k miles of wear, it's going to be shot or close to it. Might as well replace it. The procedure is similar to the motor mounts, you need to jack up the transmission or transfer case using the wood cushion. There are two large bolts going up into the frame, and four smaller studs that go down into holes on the crossmember. I recommend removing the crossmember (two bolts on each frame rail) once you have supported the transmission; it is possible to do it without removing the CM but it is much easier to get the old mount out and get the new one lined up correctly if you remove the CM.
After you take off the CM just unbolt the old mount from the car, and bolt the new one in, making sure it is oriented correctly (on my '92 there is a bracket for supporting the catalytic converter that goes between the mount and the body, that makes bolting it back up a little tricky). Don't tighten the upper bolts all the way yet, some wiggle room will help you.
Now the first time, I tried jacking the transmission up high, bolting the CM on the body and then lowering the mount onto the CM, but could never get the lower studs on the mount to go in the CM holes; it was always an 1/8" off or so. What finally worked was to start with the CM unattached, then lower the transmission some and then benchpress the CM up to the mount so the studs go into the holes (you need to have the tran low enough that the studs will poke through the holes before the CM hits the frame rails), and then thread the nuts onto the studs with a socket and long extension. Once all the nuts are started the CM will be loosely attached to the tran mount but not the frame. Now raise the tran until you can get the CM-to-frame bolts in. You might have to fight with the CM to get those bolts in but you have way more leverage on the ends of the CM than on the mount, and it went pretty easily for me. Tighten those CM bolts and then lower the transmission slowly until all its weight is on the new mount. Tighten the four nuts on bottom and two bolts on top. Good to go.
Hope this helps- Rob