Welcome!!! No apologies needed for a long message, I'm much more long winded by far..

The first thing to get is the Bentley repair manual!! Tons of technical goodies with all the specs and stuff.. These can be had rather reasonably from Amazon and such...
Most definitely you need to change the timing belt and tensioner, new injectors can;t hurt either.. Make sure you use new heat shields (the little copperish seal under the injector) Since you will have the pump off for a reseal glow plugs aren;t a bad idea as they are much easier to change at that time.. One other thing woudl be a water pump.. Much easier to change while the timing belt is off.. Since you have to remove the valve cover to lock the cam you'll need a new v/c gasket as well.. The steel reinforced rubber ones are a good upgrade! They seal much better and can be reused several times..
AS far as tools, other than your basic run of the mill metric hand tools (including metric allen wrenches) you will need the tools to lock the cam and injector pump, as well as a dial indicator to set the timing.. A spanner wrench to turn the timing belt tensioner is helpful but it can be done with out..
For the timing tools the best bang for this buck is this
http://cgi.ebay.com/ebaymotors/VW-Audi-Jetta-Diesel-Injection-timing-Set-New_W0QQcmdZViewItemQQhashZitem20ae6e5dabQQitemZ140365421995QQptZMotorsQ5fAutomotiveQ5fToolsTHe dial indicator is in metric and is a very decent quality set for the price.. At the least the dial indicator and adapter are needed, the cam can be locked with a piece of flat metal, the IP can be locks with a piece of round metal.. There is also this set
http://www.dieselvw.com/VWDieselTimingBeltToolsandGauge.htm Although a cheaper option, it is just that, cheap.. Not to mention this particular seller (do a search for "Prothe") has been known to be shady.. I would caution buying any parts from him.. Especially an injection pump!!! They are at best a poor book end..
I'm sort of at a loss for parts vendors as the one I have used for years retired and closed up shop, but check out the vendors section on here.. Myke_W, Giles at performance Diesel (Burn_your_money works for him), and a few others will set you up at a reasonable price with quality parts. THey help support this forum as well.. There are a few other vendors out there such as The Parts Place that are reputable (I guess they are reputable??), I'm sure others can chime in with suggestions..