Version 1.43 was just released, and the makefile generation step is vastly improved.  You may see a slight slowdown (doubtful, but you might...) during dependency scanning.

I think I've identified yet another bottleneck in the makefile generation that is affecting your build times.  I believe at this point I can provide about an order of magnitude decrease in the makefile generation time.  I'll let you know as soon as I have a build ready for testing.  It will be included in version 1.43.

I'm not seeing a drastic change in build times except if I have syntax checks enabled.  Syntax checking causes the compiler to  be invoked in the background for each and every file in the project, which can degrade performance on some systems.  Do you currently have that enabled?

Additionally, when the project is first loaded, Simply Fortran should first calculate module dependencies, which takes a noticeable amount of time for your sizable project.  If you click "Build Now!" while this process is running, the "Generating Makefile..." message will appear.  However, the makefile construction process will not proceed until the dependencies have been calculated.  It might make the makefile generation step appear to take more time than usual, but generating the makefile itself is considerably faster once the dependencies are initially calculated.

I'll keep looking for additional issues.  Please let me know if I've missed anything.

I did want to quickly add that Version 1.42 was the first to feature GNU Fortran 4.8.0.  There's a possibility that the compiler is noticeably slower.  I'll check into it.

Is this a degradation versus Build 1173, the original 1.42 release?  I'll have a look, but it might be a few days as I have some personal things to attend to this weekend.  Sorry for the trouble.

Jeff - you know the project...  :-)