Hi Darren...I hope you didn't heat the mainshaft and gear hot enough to discolour them...if you did I would advise fitting another gear as well...
The fixed gears should be a press fit onto the shafts..though sometimes they do work lose over time.
The fit is quite 'heavy' and you will need access either to a large flypress or a hydraulic press to remove and refit them. So, head for your nearest engine refurbishment shop or Engineering firm who may have this equipment.
As you say the gearbox has to be assembled in top gear and the gear selector quadrant inside the box also has to be set in the correct position prior to replacing the inner cover.
There are also a number of other factors to be taken into account in assembling and setting up the gearbox...If you don't have them I would strongly recommend you get hold of the factory service sheets for this model before attempting reassembly to give you the information needed and thus the best chance of putting together the box so that it functions correctly. The M20 box is definitely not one you can build with intuition alone.
I believe Henk has all this on disc, for sale at very reasonable prices...Ian
email (option): ian@wright52.plus.com
Hi Darren... You will be OK with 100 degrees....
The factory work sheets show a picture of the gear cluster set in the top gear position. For each shaft there is a selector fork and selector dog. On the mainshaft this is fitted between top (4th) and third gear. Top gear is the gear that fits through the gearbox bearing, third gear is the one on the other side of the selector dog. On the layshaft the selector dog is between second and first gear. First gear is the one nearest the kickstart end. Second gear is on the other side of the selector dog.
When the gearbox is set in top gear the selector dog on the mainshaft is engaged with the dog teeth on top gear.
The selector dog on the layshaft should then be positioned between first and second gears...hope that helps, but look for the illustration in the service sheets...Ian
email (option): ian@wright52.plus.com
This is what the cluster looks like in 4th gear. Set it up in your hand so that it looks so and then shove it into the box...then start all over again....at least that's what I normally have to do 
Pete
email (option): petercomley@web.de
hi, them shafts look like brand new, pity about the rusty deposits on the gear pinnions,my dog is now dead
email (option): richardholt@rocketmail.com