Need help in improving a FORTRAN application

I agree that some more information about the purpose of your work would help, anyway, I suppose you are going to write code in the fortran 90/95 standard, not the obsolete fortran 77 -this can be viewed already as the first suggestion- since good free compilers are available also for f95 (gfortran, g95);

For point 1 I can suggest a couple of links:

http://www.metoffice.gov.uk/research/nwp/numerical/fortran90/f90_standards.html
http://www.mad.zmaw.de/fileadmin/extern/IMDI/WP2b_coding_rules.ps

which give mainly estethical suggestions about how to write readable Fortran code, probably not everything should be taken literally, but you can learn something useful.

For a more advanced approach, I suggest the link about writing Fortran code in an object-oriented way:

http://www.cs.rpi.edu/~szymansk/oof90.html

and, if you can read Italian, though I am afraid not, then a link of my own:

http://www.webalice.it/o.drofa/davide/f90/slide/

The most basic suggestion for writing good Fortran 95 code is: use modules!

Concerning point n. 2, I have experience in using automake/autoconf also for managing Fortran projects, but this makes sense mainly in an Unix-like environment, I can give further information if needed; for a simpler and more hand-made approach using makefiles, see again my page, this time in English:

http://www.webalice.it/o.drofa/davide/fortran_corner_en.html

at the Makefile-fortran section.

For point n. 3 I suggest compiling using profiling options (how to do it depends on compiler, but most compilers do have these options), in order to have runtime information about how many times every subroutine is used and how much it costs in terms of computation time; this practice is more or less the same for Fortran as for any other compiled language, such as C or C++.

Point n. 4: this really depends on the purpose of your program
Point n. 5 depends on the platform and operating system you are using, unless you mean the existing fortran standards; concerning fortran standards I can say the following:

F77: old standard not suitable for modern code, but still many legacy code exists written in this standard
F90: a big change with respect to F77, allows more readable and structured code (free format, MODULES)
F95: very little changes with respect to F90, most compilers including the free ones support the F95 additional features, so F90 and F95 are almost synonims nowadays
F2003: up to now it is mainly a standard on paper, but some commercial compilers which partially implement the standard are starting to appear, I suggest you to neglect for starting

In general the standards are backward compatible, apart from very obsolete features, so a F95 compiler can compile also most existing F77 code.