Dear Pavlo,
ad 1.: Please check + correct following Troubleshooting, 2.1.19 Problems reaching convergence and understanding ATENA convergence parameters and 2.4.6 Floating point problems - Division by zero, Loss of >7 digits on the matrix diagonal, CCFEModelExc: CCPardiso solver error: zero pivot, Warning: Sign of diagonal changed when reducing equation, Floating point exception: Multiple floating points traps, Zero or negative jacobian, InvertA: zero determinant, CCMaterials Extended AExc: CC5ParamYield F: project_stress_on_f_division by zero, and similar.
If you still have problems, you can follow Troubleshooting, 2.1.1 to sen us your model etc.
Ad 2.: You can see some information in GiD under Mesh - Mesh Quality. However, the basic (=most critical) for most volume and surface elements in ATENA is the edge length aspect ratio (to be kept under 2-3:1). The next are the angles (shown in the Mesh Quality dialog in GiD) - narrow angles are problematic, from about (20-)30 degrees OK.
Ad 3.: Most of the convergence errors are global measures (for more information, see Troubleshooting, 2.1.19). Moreover, problematic elements or extreme stiffness ratios typically make the system conditioning ill, which results in degraded precision / numerical problems globally (not just localized at the problematic regions).
If you see unexpected localizations at the M-S connections, I suggest to make sure the orientation of the connection is as recommended (side with coarser mesh as Master; for comparable element sizes, larger surface as Master).
Ad 4.: No special guide is recommended :-) 1-D bar elements can be used in Shells the same way as in Volume elements (with the exception of the older Ahmad Shell elements and bars in thickness direction, which would make no sense due to the undeformable thickness of these elements; we generally recommend the newer IsoShells). Moreover, you can freely combine reinforcement layers and discrete bars.
Ad 5. We are continuously working on performance improvements of ATENA Studio (and also of the solution kernel), however, with such an extreme model, I am afraid you can not expect instant response...
I suggest to see ATENA Troubleshooting, 2.2.17 The analysis runs too long. How can I speed it up? and 2.4.1 Out of memory error during ATENA analysis for basic related tips.