You're welcome, I'm glad I could help inspire an improvement to the software.
However, I could still use assistance, as make now fails much later into the compilation. I copy and pasted the example Trilinos configuration script you linked to into my Trilinos reconfigure script, the new version of this file has been uploaded under the name trilinosReconfigure. The Xyce reconfigure script was changed to the new location of Trilinos's files (/home/dragontamer/XyceLibs/Serial instead of /home/dragontamer/XyceLibs). I then reran the reconfigure files and make, make install commands for Trilinos, and I ran the reconfigure file or Xyce and make, however, make now breaks here:
CXX Xyce.o
CXXLD Xyce
/home/dragontamer/XyceLibs/Serial/lib/libtrilinoscouplings.a(EpetraExt_AmesosBTF_CrsGraph.cpp.o): In function `EpetraExt::AmesosBTF_CrsGraph::operator()(Epetra_CrsGraph&)':
EpetraExt_AmesosBTF_CrsGraph.cpp:(.text+0x914): undefined reference to `trilinos_btf_order'
/home/dragontamer/XyceLibs/Serial/lib/libifpack.a(Ifpack_AMDReordering.cpp.o): In function `Ifpack_AMDReordering::Compute(Ifpack_Graph const&)':
Ifpack_AMDReordering.cpp:(.text+0xef0): undefined reference to `trilinos_amd_order'
/home/dragontamer/XyceLibs/Serial/lib/libamesos.a(Amesos_Klu.cpp.o): In function `Amesos_Klu::PerformSymbolicFactorization()':
Amesos_Klu.cpp:(.text+0x4073): undefined reference to `trilinos_klu_defaults'
Amesos_Klu.cpp:(.text+0x40a5): undefined reference to `trilinos_klu_free_symbolic'
Amesos_Klu.cpp:(.text+0x40c3): undefined reference to `trilinos_klu_analyze'
/home/dragontamer/XyceLibs/Serial/lib/libamesos.a(Amesos_Klu.cpp.o): In function `Amesos_Klu::PerformNumericFactorization()':
Amesos_Klu.cpp:(.text+0x4615): undefined reference to `trilinos_klu_free_numeric'
Amesos_Klu.cpp:(.text+0x461f): undefined reference to `trilinos_klu_factor'
Amesos_Klu.cpp:(.text+0x4a6f): undefined reference to `trilinos_klu_refactor'
Amesos_Klu.cpp:(.text+0x4bdb): undefined reference to `trilinos_klu_rcond'
/home/dragontamer/XyceLibs/Serial/lib/libamesos.a(Amesos_Klu.cpp.o): In function `Amesos_Klu::Solve()':
Amesos_Klu.cpp:(.text+0x5602): undefined reference to `trilinos_klu_solve'
Amesos_Klu.cpp:(.text+0x5971): undefined reference to `trilinos_klu_tsolve'
collect2: error: ld returned 1 exit status
Makefile:785: recipe for target 'Xyce' failed
make[3]: *** [Xyce] Error 1
make[3]: Leaving directory '/home/dragontamer/builds/xyce/build/src'