we have the same problem solved since 2.6
we ha a start.exe and a datadic that organices all menue and aplication parts.
we started using stonefiend and modified it a lot in 2.6.
today we are using stonefield and visual extend.

each menue item start only a sindel app.
each app is a singel projekt. so update etc. is no pain.
everything is manged for all our customers in in central databas. we can genarate alll files and DBF etc wuth a singel comand.
saves you live

D.Bachmann