If you go with polikuo's option D, then you'll also have to do option A, because the boot scripts are built-in and run before extensions are unpacked.
For option A (
see remastering guide on the Wiki), you really are installing things to RAM so this isn't really off-topic. This way you avoid the "symbolic links" bottleneck and could also trim down/eliminate lots of stuff in the start-up scripts (depending on what you're actually doing of course) - specifically /etc/init.d/rcS and /etc/init.d/tc-config. Maybe adjusting the compression settings for the initramfs when you remaster it may speed up boot, but whether to increase or decrease compression depends on whether the bottleneck is the CPU decompressing the data, or actually reading the data from the flash storage.
Bare minimum if you just want the Linux kernel to run one program, with no other processes started and only built-in kernel modules available, is to edit the boot command line adding "init=[program you want to run with full path]". You'll still need to remaster in order to include the program you want to run in the initramfs. Whether that option is even remotely suitable depends entirely on the details of your application. It's the fastest way to run
something in Linux, but you'll probably run into odd problems unless you know absolutely everything that your program is doing (preferably, you wrote all of it yourself with this in mind).
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