I am guessing you have seen this (the original was not complete; this link is).
http://www.thelolaregistry.com/DIY/Weber.htm
The Factory dump tube needs to come out for good (the stubby tube in the pliers in your pics) and yes, the hole needs sealing (circled yellow and then red in your pics).
This Lola registry article is pretty much how most people do this (including Ivey from memory). I must have done about 9 carbs just like this now and they all worked fine except for the second hand one that I missed seeing a crack in the body. The new 1/16" hole dump tubes are fairly floppy and easy to bend by mistake when you take the top off; if they are in the wrong place the mixture is all wrong. Don't use the 3/32" hole size tubes; they flow too much and run rich. You should be able to get your mouth onto each dump tube and blow through them equally.
The secondary needs to be cracked open a bit; adjuster is hard to get to when all mounted up.
When you say the primary is too rich; how do you know? Is there raw fuel visible coming out of some place (dump tube, venturi etc). Is the actual mixture adjuster (side of carb) accidentally closed or wide open.