I'm just in the process of completing a similar conversion to Martyn's old car (all be it using Zetec instead of the x-flow) but the answers will be the same:
First-off gearbox selection -
There are several variants of the Type-9, the Sierra V6 cars have a taller 1st gear but a long input shaft which will not be suitable for use with a x-flow without a bell-housing spacer which will stuff up the engine positioning/mounting brackets.
A standard type-9 1st will be very short as stated by others above and this can be seen if you have a chance to drive a CVH 4/4. However the Standard Type-9 is the correct length (casing) and a suitable bell-housing is easily sourced including alloy versions which are quite nice. All type-9's have a larger output shaft which means whilst you can re-use your prop you will need to change the gear-box end of the UJ to a larger one - again easily sourced and fitted.
Starting from the engine end of things. You can probably get away with using the same clutch, flywheel and starter. However you will best off replacing the slightly heath robinson clutch release mechanism for a concentric hydraulic one. To do this you can get a kit of parts from Retro-ford and using a brake master cylinder spacer (available from Morgans) you can mount this to the clutch pedal.
On the later chassis, you can lift out the gearbox and remove the mounting bracket from the chassis (it will need to be moved back - welding may be needed).
The gearbox cover may need some adjustment in terms of the location of the gear-stick - but I don't think much. Quaife do a decent cranked gearstick & quick shift so ditch the stock ford unit that has enough slop to do a good impression of a soup bowl.
Photo's for the above I can post as it's undertaken in the next week or so.
For you, the important consideration is that of the innards of the gearbox. Trans-X and Quaife do gear-kits or you can always have the V6 1st installed if the rest of the ratio's suit you (easily used calculator available from Gearboxman website).
For road use, a helical or semi-helical set is available, I can tell you now a 2.2:1 1st is too tall for all road going morgans and it's better off going for a 2.39:1 when using a 4.1:1 diff.
You'll need to find and source a suitable spedo drive. The quill drive that the type-9 units use is not easily sourced and it may be easier to retro-fit a hall effect sensor and pulse driven speedo (which will get rid of the spedo wander on older cars).
Upgrade options:
Depending on your budget and appetite (not for the faint hearted). You can take this upgrade some distance. At a base level both Quaife and Trans-x (now the same company as of a couple of months ago) do not just gear-kits but complete boxes off the shelf. The Quaife unit being the QBE13Z if you go onto their web-site. This however uses a steel maincase.
Heading further up the ladder you can get from Quaife a fully Alloy cased unit which is a lot lighter which is the QBE15Z both this and the 13Z are available in a variety of custom ratio's.
Right at the top of the ladder is the Quaife G50,55,60 which are either H pattern or sequential mechanical shift Type-9 replacements which Quaife have custom designed from scratch.
Other things to consider:
Ditching the standard flywheel and clutch. Both of these units in stock form are very heavy and if you ever calculate the rotating masses effect on the effective weight of the car, loosing the KG's off these components will make a massive difference in the experienced performance of your MOG!!!
A lightweight fly is easily sourced and there are many suppliers, HELIX, AP, Master Clutch, Mister Clutch etc. etc. who can supply lighter single plate clutch packages. You only need to install the correct amount of spacers to get the release bearing in the right place. Clarefull measurement and ordering from retro-ford/burton can get this sorted.
Hope this helps!