Not sure if you've done this kind of thing before, but just in case... Take photo's of everything from every angle before you touch them, it makes it very much easier to figure out how it all goes back together!!
Regarding the brakes, have you checked whether the "wheel" components have also been changed? If so, and depending on what has been fitted, the original master cylinder might not actually work without returning the entire system to "factory". And have you ever driven a Series 1 with the original brakes? When functioning at 100% they work well enough to pass rego, but can still be "interesting" in modern traffic! As you've already specified that you're not doing a full restoration, why not keep the later system? Especially as the current motor, and your planned replacement, are more powerful than the original. If you fit bigger wheels/tyres than the original 6" ones, you'll also have an increase in rotating mass for the brakes to fight against!
My 86" at present has a Holden motor, which under current legislation must have an engineering inspection and mod plate (unless you want to try to argue legalities of 1970's regulations and when the conversion was done) and when I discussed this with the certifier he specifically stated that he would expect a brake upgrade to accompany any increase in power, even if gearing - and hence speed - was unchanged. As the 200tdi would also require "engineering" (no chance it was done under the old regs!), you might face the same issue.
In answer to your specific question about linking the original master cylinder to the remote booster, some time ago I discussed this with a supplier of brake servo's and he told there is an issue with the booster being physically higher than the master cylinder. I recall it involves fluid draining back through the system as the diaphragm moves, resulting in a "long" or variable pedal push. Apparently it can be minimised with a modification to the booster but it is preferable to keep the booster below the master cylinder, which is hard with the Series 1 "under the floor" system! I wouldn't like to guess whether this actually relates to the master cylinder or the height of the fluid in the reservoir, at the time I was discussing another vehicle with it's own issues!

