A few ideas:

1) Loading a lot of modules can be slow. You are already avoiding that by using 
racket/base and racket/gui/base, so that's good, but it already takes me 0.5s 
just to require these :-( . I don't know it there is much to do about this.
2) Your main.rkt might be doing a some lengthy initialisation work. Try 
inserting a displayln right at the beginning, to see if there is a long delay 
between that and the moment when the window pops up.
3) Of course use raco make or raco exe (from your README I gather that's 
already the case).

Try also comparing with the start-up time of the simplest GUI application you 
can think of, e.g.

#lang racket/base
(require racket/gui/base racket/class)
(define f (new frame% [label ""] [width 100] [height 100]))
(send f show #t)

Hopefully someone else with more knowledge about racket/gui and/or optimisation 
will give better recommendations.

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