Magyar,
I'm nearing the end of my 3000 restoration, and all I can say is, you can't have too many pictures of how the car is supposed to look and how everything is bolted on in the first place. The probelm with putting one together from boxes of parts is that you do not have the pictoral guide that a good set of diasassembly pictures offers. In hindsight, I would have taken about 200 more pictures. Get all the books you can. Workshop manual, body parts book, mechanical parts book, concourse guidelines, Haynes Manual (yes, the Haynes has info that the workshop manual does not) Moss catalogue (yes, somehow the Moss Catalogue has parts diagrams not found in the parts manuals) Roger Moment and Gary Andersons's book, drivers handbook, the large laminated Healey wiring diagrams that are available on line at ebay, the nuts and bolts inventory that some dilligent person put together for every nut and bolt of the cars (not sure how to find them again, I got them off the List) I often refer to many of the above for an hour or two before I bolt on anything.
After doing this for years, I arrived at the following approach that ended up working well for me. First, do the chassis, as shown above. I had a restorer do mine. Once you have something that is solid, you move on to the body panels. Get them all to fit right. Once they all line up right, you can think about painting them inside and out. What I am telling you to do is to remove the panels once you have them all fitted the way you want and then paint eveything inside and out. Again, my restorer did it this way, and his work was nationally recognized. Now place the body panels aside where they won't get hurt because it is time to install the mechanicals. Start with front and rear suspension, followed by brakes and brake lines, electrical harness, electrical components, under dash stuff, engine and transmission and drive shaft, followed by manifolds and engine ancillary parts. Now the body panels can go back on and then the lights can be installed and wired. Some of the chrome can go on at different times, but I put mine on after all else was hung on the car. Interior comes next and the top comes last.
Before you put on anything, ask youself "what has to go on before this?" Even if you are careful, there will be several things you take off after you have installed them because something else should have gone on first. For me, i have a beautifuly installed exhaust system that I will have to partially diassemble to install the seats, because the nuts that hold downt th eseat rails are pretty much impossible to reach with the muffler installed. That's just one example. There are hundreds more.
For each assembly or sub assembly you are going to install, get the parts book out and make sure you have every part needed down to the washers. The parts books give codes for the hardware and you can use the Moment/Anderson book to make sure you have the right size and type of fastener before you start installing. The list mentioned above gives even more information on hardware. Anyway, make sure everything is the right size and in the condition you want it to be in before you put it on the car. Assemble it lose and then stand back and look at it before you tighten it up. Is it in the right place? Is something else supposed to connect to it? Can you reach the area where the next part has to go?. Once you are sure, then tighten it up.
If you paln to use new modern hardware, your life will be a bit easier, but some of the sizes may be hard to find. If you plan to use the original hardware, send it off to be replated. Check the condition of the hardware before you send itout. It makes no sense to wate monwy replating stipeed, bent or rounded bolts, etc.
If you are painting the black bits black yourself, be sure to strip the part down to bare metal. A parts cleaner followed by a blast cabinet is good here. Once the part is blasted to bare metal, use a paint prep chemical wash and then dry the heck out of the part and prime it twice. After the primer dries, paint it at least three coats. I use a halogen light as a heat lamp and put the painted parts about 18 inches to two feet away from the lamp and bake the paint on. This results in complete drying so that the paint does not transfer on to the car or other parts that you bolt the newly painted part on to.
Those are my general tips and advice. I hope it helps. Good luck, and see you on the other side.