1. I cut them off the tree using a Dremel tool. What would you have used ?
Hacksaw either junior or full size for the larger dia fittings
2. I marked the centres with a centre punch. I did it by eye but is there a more accurate way to find the centre ?
File ends flush with the lip and also tidy up the lip if teh two moulding halves are out of line. Apply marker pen and then eyball centre before punching. Preferably a light dot punch first and if its in the right place enlarge the mark with a centre punch.
3. I then used a centre drill but I found that I was never quite in the centre ! I think my centre punch mark was slightly out but at this stage I do not think there is any way to fix this…or is there ?
No need for a centre drill the drill bit will locate OK in a punch hole
4. I drilled out the fitting with a 4mm drill. Charts on the internet show this is the correct tap drill for 3/16-40 ME. I did this with a hand drill. The big problem here is holding the fitting in a vice without damaging it. I was using aluminium soft jaws but these can still squash the fitting out of shape. Any suggestions to solve this problem ?
4mm would be right. I do them in a bench drill (actually mill used as a drill) this would help keep things square rather than a handdrill – was it hand powere or just a handheld cordless? I just use my mill vice carefully and when doing the second hole put a bit of threaded aluminium or brass into the other hole so you don't crush the fitting* You can also use the same rod when setting up the fitting for the second hole by eyballing it horizontal the the second hole should end up at right angles to it, I'm using a tap here to do the same thing but a rod would be safer for you incase the drill hits it.

5. I then used carbon steel taps to cut the thread : taper tap then plug tap…no second tap. Some of them turned out okay but others were not quite square. Is there a ''bodge'' to fix this once you have already cut the thread ?
Carbon taps will be fine, use a second if you have it as its easier to get a deeper thread particularly on the blind holes in elbows. If you do have a bench drill you can leave the part clamped under the machine and then use the chuck to guide the tap which helps to hold it vertical.
* Some people make nesting jaws or jigs to hold the fittings but as you don't have the equipment we will forget that for now but for interest have a look at this and this
J
Edited By JasonB on 14/09/2014 08:11:12