My 98 rm 125's water pump seal is leaking and it needs a top end rebuild are their any good online guides or videos to help me do it?

It all depends on where the water pump seal is located... most are pressed in from the outside... pull it down until you see what needs to be done... whats wrong with your water pump?? - why are you rebuilding it?? is it leaking?? ...

Typically the whole pump is replaced, as there is commonly a bearing failure also...

It sounds as if you have rebuilt the engine without torqueing the head bolts. Although, it could be that the cylinder base gasket has been torn during the rebuild. Try to re-tighten the head bolts to the correct settings first. Good luck.

If it got realy hot you may of warped the head or cracked the cylinder. Do a compersition test to see how much pressure you are looseing. High would be the head witch would be easyer and cheaper to fix low you may need to replace the cylinder

Did you do the reassembly yourself? If not, take it back to whoever did because the reassembly was done incorrectly. Oil and water mixing can only happen at the top or bottom ends of the barrel. Either the head gasket is not seated properly or the barrel to casing seals are not properly installed

yes, you need a special tool to split the casses and a tool to remove and install the crank...

It should be just that, a leaking seal, gasket. The water pump is external on that bike and doesn't go anywhere but the cooling dept.It doesn't get mixed with oil or anything. Take off the pump itself and replace the gasket. I think that should do it, unless it is the pump itself leaking.
Suzuki RM125 RM 125 Water Pump Housing,,,,
That is an ebay ad. Just in case. Hope this helps.

1. you may have problem with the number 33 seal this is basicaly the most common problemme with water pump leaking hole
   

It has seals there for the water pump. They need to be replaced.