Glad you are enjoying the build Nino.

Let's look at some of your initial observations, let me first say that all of your points are covered in the electronic manual - it is 56 pages with LOTS of pictures:

Bag 9 has a 10K resistor leftover. This would be R14. I can't find it in the doco.

It is R14, shown & mentioned in manual - ommission on the checklist, will correct.

Page 5 - Microprocessor selection chart for 6800 - Use the jumper HPJ2 - The holes are present, but not much of a solder pad. This may be an issue with connectivity. It looks to be the same for all jumpers. I would like to suggest larger solder pads.

This is actually the way the PCB factory read my files - basically it's a cockup but it is also covered well with pictures in the manual that show how to connect them correctly as are the new transistor pads - the manual suggests ignoring the new holes for the transistors and using the original ones.

Page 6, the Capacitors are listed, but not where they belong on the board
C14 - 470pF (471)
C15 - 470pF (471)
C16 - 0.1uF Greencap (104)
C18 - 0.047 (473)
C32 - 0.003 (332)

Several pages in the manual give this info with lots of pretty pictures.

Page 6 - installation of Q1, Q2 and Q5 - The original solder holes are fine - that's how I installed them. The new holes are too small for the transistor legs and there is hardly any solder pad to mount them.

Yep - as above

Page 6 - 82 Ohm 2W resistor. The rightmost eyelet is VERY close to CR5's solder pad. I didn't use the eyelets.

The right leg of R11 and the top leg of the diode CR5 are actually connected so it doesn't matter if the eyelet touches. Actually it's a pity you didnt use the eyelets because I spent two solid days tracking them down feeling that they add a lot of robustness to the mounting of R11 - never mind.

The advantage to building this board is you can tailor it to be your own. Change things, leave things out, use different micros, memory, battery backup options.

There are about 20 other small things that we have already tweaked for the next run of boards and I'm not telling what they are  .

Remember the checklist is just to help assembly - it is not meant to replace the manual and tha manual is where we concentrated our main efforts. The manual is currently supplied on a T-Flash memory card with an SD card adaptor included - this may change as we tweak things.

You really should at least skim through the manual Nino - there are a lot of subtle things that are mentioned including pitfalls to avoid.

Are you building it for 2716 or 32's?