It's your syncrhos. Just tell the dealer that you have problems with them and that they need to be addressed. It's a known problem with the 5sp's and my dealer basically told me that he'll see me in another 50-70k.
I had mine replaced in Aug 00 and they are still working rather well, just about 20k on the truck since then.
Do a search for synchros and you'll see that many of us have had the same problem.
Fwiw, my truck was in for about 22 hrs of shop time, plus time to get the parts, so get ready to make some alternate travel arrangements, or get a loaner that you like (ie: not a focus!)
hth.
Bambino
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Bambino Worldwide
Owners Gallery Truck #179
1999 reg cab/short box/ORP/Silver on Dk Graphite - 3.55; 4.6l 5sp; Factory Tonneau; 40 chan CB/Maxrad Antenna; Kicker amp'd sub tubes; Rockford Fosgate components up front; Custom Exhaust; Mobil 1 5w30/Motorcraft FL820s; Amsoil Series 2k in the driveline.