If you feel you have to take the trans off first, put a jack under the trans, then remove the trans crossmember. You can then let it sag down a bit so that a sicket with a U-joint can reach the bolts.

However, if you remove the front clip first, it just has to be easier to remove engine and trans at the same time. Just take a close look at what's going to interfere, and attach your hoist chains accordingly.