manta

In your first step, you dissolve 10 nmoles of a primer in 200 ul.  This gives a 50 uM solution of that oligo.  Now there is another oligo in the tube, and the solution will also be 50 uM with respect to that oligo.  When they anneal (assuming they do) you still have a 50 uM solution of the pair.  I would call your 200 ul of solution a 50 uM solution.  The rest of your calculation looks correct, but I would interpret the paper as meaning a 1.5 ul addition of the 10:1 diluted stock (i.e., twice as much as you are currently using).  Having said that, there is usually excess primer, and if things are working (which they probably will be) then go with it.

In diagnostic lab I did my thesis in there was always isolation control. It tested that samples were not contaminated during isolation procedure, I think it was an empty sample of water isolated together with other samples that day.
Also a positive control to test if your mix is OK. NTC always. I'm not sure if you really need RT- control, it's a RNA virus you detect or transcripts of DNA virus? (if DNA, then it's a question why are you not amplifing it's DNA, but that's reason can be detection of the transcriptionally active virus only). Can your RNA have a DNA form? If not I don't see reason for RT- control (but I may be mistaken).

Usually standards for viral RNA detection are created as in vitro (I think) transcribed RNA from expresson vector containing your amplicon (so no actual virus), dilluted (not sure if with some junk RNA as is done with DNA standards, depends how much other RNA can be present in plasma) and stored -70. Reverse transcribed with actual samples. If it's a common virus you can purchase standards. I'm not sure if you can use serum sample quantified with spectrophotometer, it may contain other RNA than your virus.

I was doing DNA viruses, so I only looked at all this, but I often said to myself I'm glad I don't need to mess with RNA standards. Lots of quanĺity testing required, you need to be sure your standards are not degraded in time.

I'm not used to magnetic isolation, but yes, leaving the particles in may cause problems. If they are magnetic you don't need to centrifuge them, just get a strong (neodyme) magnet to attach the particles to the tube wall and pipet the rest out. The particles could be so little to centrifuge anyway.
But if your machine broke in the middle of extraction there is really question what you have in your tubes. I would test a new properly prepared sample.

You can check te RNA on spectrophotometer, but that will only tell you concentration and purity. Use a NanoDrop or similar spectro, that can measure in 1-2 ul. Diluting 1 ul in a 100ul cuvette won't work, the reading would be too low.

To see better the condition of your RNA you should run it on denaturing gel (get a protocol), you will see 28S/18S ratio and bands distribution and (roughly) DNA contamination. RNAse free (DEPC treated MilliQ or commercially nuclease free water) is generally recomended for all solutions, but since there is formamide or formaldehyde put into gel or the sample, we don't bother with that in RNA electrophoresis. With DNA ELFO we just use buffers made from destilled tank (we have 10 L barrel for TBE). For other solutions not made in such a large scale we use autoclaved MiliQ.

I would throw out all the solutions and make new ones. Especially if you will be working on thousands of samples. It's not worth the risk. But I'm not sure if just your MiliQ water is considered RNase free or you need to treated with DEPC first. Only autoclaving won't work either. You can never be sure enough with RNA, especially if you want to store it.

To save your primers first check if you really have RNA, then check the cDNA with some common primers (like beta-actin for human and mouse) to see if RT works and THEN make your reaction. Nuclease free water (or just at least autoclaved MiliQ) all the time. If you not sure in what conditions there are now, aliquot the storage concentration in small volumes and keep it -20. But if you check every step (RNA? cDNA) OK and you still get no bands on positive control, you have to think about reordering. It's really difficult to check whether primers have degraded or not. I resuspend my primers not in water, but 10 mM Tris pH8 (made with autoclaved MiliQ) that makes it more stable, my primers once degraded even in nuc-free water, is a selfdegradation due to pH, can happen sometimes.

There is RNase Zap from Life Technologies but I'm not sure whether you can use it to clean the machine. I'm not really a chemist, but I would be afraid H2O2 is also very oxidising and could damage it. Better ask the manufacturer what they recomend for cleaning. Otherwise rinsing it repeatedly with water and 70% EtOH is enough for some people, but I think there may be questions about efectivity against RNases. But I would care primarily about the RNases in my solutions.