Basically nice shots already. I second the previous posters comments on exposure and how it affects color, as well as RAW capture, both essential for fine tuning color.
Some additional random thoughts ...
You got quite creative with your lighting, but possibly introduced more problems than you intended. Consider that the camera can only adjust color for one light source, but you use fluorescent most likely at 5500-6500 K, which have squarish peaks, as well as room light with around 2400-3000 K, a black body radiator. The two light sources are not coming from the very same direction, so some areas of the flowers receive more of the 6K light, some more of the 3K light. The consequence is different color renditions in different portions of your image. Black you can block out, but anywhere else it will cause problems.
You do want to shoot with light sources of one and the same color temperature (unless you intentionally want to have freaky color effects) and to be of a black body radiator type (so not fluorescent tubes), then white balance the camera for that light source, then if you still need to make adjustments, do them in RAW conversion.
I have tried to do color temperature measurement with an external meter (Minolta Color Meter III), then set that manually in the camera (can be done in some models). For macroshots, this has resulted in worse color than auto white balance. I was rather surprised by that.
For consistent exposure, consider purchasing a neutral grey card board. Today some also come with a grey scale wedge, so you can use zone system to check and adjust exposure.
If you are picky about color reproduction, you may want to look into proper color management. It starts with custom white balance when you take the shot, to spider calibration of your monitor(s), to using proper profiles for printing.
Real World Color Management is quite good. I use a Pantone ColorMunki for profiling everything, from displays to PP projectors. Makes a truck load of difference.
When sharing on-line, however, you don't know what the viewer at the other end is using, so that can lead to pointless discussions on webforums.
If you are concerned about the interplay of brightness and color, then consider looking into Lab color space editing. I like it a lot. See also
This Book, which I like. Not sure Lab is supported in Lightroom; I rather use Photoshop. You may also need PS for making illustrations for your thesis and for papers; it's been my main workhorse for quite some time. My first digi-image pub was in 1998.
Re problems with manual focus of some poster, consider using a third-party matt focusing screens (Beatie, Haoda, etc.). Those can be user interchanged on some cameras. I use one on my Canon 5D mkII and MF Zeiss glass. Live view with the option of zooming in (digital version of the old focusing loupes) helps tremendously.
In macro, also be aware of focus shifts when stopping down the lens, so you may want to examine the aerial image with working f-stop. In the viewfinder, it darkens the image significantly, but on an LCD screen, the camera will compensate.
Linear Mode
