The engines are very different but as the bellhousings were separate(unlike later Fords where the b/h is integral with the gearbox) But you have 2.3 and 2.8 early Cologne's from Cortina's,Sierra's and Granada's with carbs or MFI then later Granadas had a 2.8 with EFI and all of these are two port exhaust heads and 2.4 and 2.9 EFI's with 3 port heads not only this the early Explorers came with a 4 Litre Colonge based engine too.
Essex engines are either 2.5 or 3.0 and a far torquer engine than the Colonge.
Gearbox wise you have early Essex with a Type 'F' box with or without overdrive whilst later ones had the Type'5' without the o/d(Scimitar all had the Type' F ' even with the Cologne SE6b and SE8) Most of the Colognes got the Type '5' box
Later 2.8 Capri's also came with the Type'9" five speed box and if you find the correct bellhousing you should be able to 'mix a match' so to speak!
Auto boxes were the Borg Warner Type 35 on early Essex and Ford C4's on later and all 2.3/2.8 Cologne engines and the last Essex got the Ford C3
The 2.4 or 2.9 came with the A4LD or A4LDe 4 speed autobox after I think 1989
Hope this is of help