Try loosening all the mount bolts and giving it a good jiggling to see if anything seats itself.

I had to do that to a ford probe with a MX6 engine and trans. FYI anyone that does this with a probe remove and install the engine and trans together.

Fords are a little different (cheaper). Most are built to have the engine, tranny and basicly the whole front end lifted into the engine bay from underneath during inital assembly. They never gave much thought to R+R of the engine or tranny apart (ANY thought for that matter). Ever try to do a clutch in a mid-90's Ford Tempo? It took me 4 hours before I gave up and dropped the whole engine/tranny/front end.

In contrast, my favorite job was an '89 Acura Integra. The thing was so damned well designed, I did a complete clutch job in 2 hours.

I loosened all of the mount bolts, wiggled the engine, and pried the transmission with a scrap of wood. It seems quite a bit better, and I got the cross member in place. I guess I'll call it good. I've been working on this thing since 11 AM...it's 1:15 AM now...Must go pass out.

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1979 240D- 316K miles - VGT Turbo, Intercooler, Stick Shift, Many Other Mods - Daily Driver

1982 300SD - 232K miles - Wife's Daily Driver

1986 560SL - Wife's red speed machine

Aw, come on. I was up for 42 straight hours until I finished mine.
Got up at 11am on Saturday and went to bed 5am on monday.
I have no clue how I did it. No caffeine, no naps, and 1 lunch break. Just plenty of drive to get it done.

Wow, you're crazy. I had to cut an inch out of the down pipe to get it to fit. The weld looked like moldy cheese. That was my cue to end for the day.

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1979 240D- 316K miles - VGT Turbo, Intercooler, Stick Shift, Many Other Mods - Daily Driver

1982 300SD - 232K miles - Wife's Daily Driver

1986 560SL - Wife's red speed machine

You shouldn't have to. A stock 300D downpipe should bolt right in.