If you took the "Intuitive" ability for your custom race you get a bunch of research points at the start, which would be why you got several techs.

If a shipyard is further than 6 tiles from a planet, a colony ship in that shipyard cannot take population from that planet.  If all you had were distant planets as sponsors, you could build colony ships, but not populate them.  You could fly the empty ship to a planet and pick up people that way.

Ah, yes. Thanks folks - it's all becoming clear to me now. Turns out that I'd selected a different planet to sponsor it. Can a planet sponsor two shipyards, just out of interest?

So, no faction-wide tax rate? I remember you could prioritise Military/Social/Science on-world in GC2 (with any unspent production being converted into cash), with the tax rate being a money in the bank - vs - growth and happiness that was set faction-wide. Does this not exist anymore?

The production wheel in empire governance puts the economy into three categories, wealth, research, and manufacturing.  Doesn't the wealth portion represent the income in taxes?  Would it work for you if they labelled that category as "taxes"?

The wealth portion doesn't represent income in taxes neatly. The entire production in wealth, research, and manufacturing represents government-directed economic activity and does not account for the vast consumer sector in any way, even though by rights it is taxed income from the consumer sector that allows government to be economically involved. If wealth were truly just a form of taxation, it wouldn't compete with production and research.

Frankly there is a much simpler way of running the in game economy. Each unit of manufacturing capacity should produce 1 BC of GDP, while what is currently called "gross income" as produced by Market Centers and the like could be renamed "Services" and likewise create 1 BC of GDP. Trade should likewise be its own sector of the economy with each unit of trade producing 1 BC of GDP. The total tax income on each planet (you should be able to set a different tax rate by planet) would be the tax rate times the sum of products and services. Each unit of manufacturing and research would cost 1 BC to operate, subject to any cost reductions brought about by technology. Maintenance costs would remain as is.

Base morale could be multiplied by the square root of untaxed income, then affected by the other modifiers. For example, a 36% tax rate on a planet with morale of 5 and population 6 would result in an approval rating of (1-0.36)^0.5*5/6 = 66.7%. Untaxed income could, of course, be boosted by creating services buildings which would impart minimal maintenance. Thus economy and morale would be connected and the game would become simpler.