G'day steve.
It depends on the ammount of FORCE you applied when bringing the two halves together if everything is working it should be o.k..
The first thing to do before bringing the two halves together is to set the Front half level ,do this by tapping wooden wedges between the front axle beam and the housing ,this steadies everythingand will make it easier to work with,I find it easier to block the front half and bring the rear half forward and when you get near the guide studs mentioned you will have to possibly adjust the wedges to get everything lined up.
The way to asssemble without damaging anything is to First line up BOTH PLATES to do this you need a clutch aligning tool that has BOTH the pto and the transmission Diameters on it .
Use TWO or FOUR Equally spaced long guide studs screwed into the gearbox side they are 7/16 UNC thread x and should be ideally 4 " long when bringing the tractor halves together use the guide studs to help line everything up, constantly measuring the gap between the two halves and keeping them Parallel ,You should not have to FORCE anything, make sure the transmisssion lever is in neutral and the PTO LEVER is set at the ENGINE position ,get someone to put an adjustable spanner on the pto shaft and slowly push the two halves together and at the same time turn the pto shaft back and forward you will feel the pto engage,when engaged THE PTO WILL NOT TURN when fully engaged put the lever in neutral and select the transmission second gear high keep pressure on the two halves and at the same time using a large screwdriver slowly turn the engine ring gear using a big screwdriver and you will feel the gearbox engage again you should not have to force anything fit all bolts and the job is done
Dont forget to adjust the clutch clearance Before testing out.
Happy Days.
Hutch.