Well...
the reason for longer forks is to alow a softer spring (which can be softer because it has a longer stroke to absorb the energy from a bump). This means the fork can be soft enought to respond to small bumps, but still have the travel to take a big hit. If you reduce the length of the shock by lifting it in the triple clamps (which would be possible it you repositioned the handlebar - yes spacers are available) then you would need to reduce the travel of the fork by limiting the stroke with shorter/ stiffer springs. Dirt bikes that are converted to dirt track/ super motorrade (sp?) often go this route.
I think the main issue remains matching the front with the rear. Yes the R100GS forks are a bit longer, but not enough to upset the handling of the bike.
The way to do this conversion is to get a full front end, with brake, wheel, and forks. This way the only issues becomes matching a master cylinder to the new caliper. BMW sells lots of different sizes that bolt onto the stock lever. You might also run into problems getting the headlight, indicator lights, and guages to fit on, but this is all do-able. The advantage of the R100GS fork is that everything more or less bolts on in the right spot.
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