Can six speed gearbox be fitted into yamaha r1 1998 model

how lucky do you feel? You will be the first one to try it. If the bell housing fittings are the same, and the transmission out is the same, you might be lucky. However, it the old one has 5 gear meshes, and the new one has 6, it has to be bigger. Better to have the old one rebuilt, or buy a 5 speed.

https://www.google.com/search?q=2001+daf+fa+150%2C+5+speed+to+6+speed+gearbox

..

Have you checked the fluid levels in the gearbox? Dropping it out of a gear takes a lot less effort than going into a gear because you've got to compensate for the different spinning speeds between the engine and the gearbox. That's the reason for a clutch.
Some automatic gearboxes are fitted with an oil filter inside them. Depending on how old the 360 is, and how hard you work it, it might be worth getting the gearbox serviced.

if it has a dip stick --through the dip stick hole

The workshop manual shows it on top of the gearbox , I have been looked for it on a 2004 model. This the has the speed sensor fitted on top of the gearbox but it has no connection (It is fitted with a yellow cap). It seems that on some models (but it is not mentioned in the manual) the speed is derived from the ABS sensors !

what gearbox of a yamaha will fit in my yamaha jog rr 2007

It means you have a problem in the shifter. Is it a five or six speed?

406 comes normally with a gearbox model BE3 of 5 speed (as limited were with 6 speed). As late models of 405 and 306 are using the same gearboxes. Mazda 2.0i zx was sharing the same gearbox (i don't know exactly the model year).
Anyway, you need the exact gearbox model to find out which car model else were built with these types of gearboxes. Manual gearboxes with same models can be exchanged from any car or van and have nothing to do with car ECUs.

Change speedo sensor located on a gearbox-if electric.If wire-check wire and dashboard instrument panel

I don't know but I suspect it will matter which port the restrictor and check valve are fitted to.

I personally wouldn't worry about the six stud vs eight stud argument. People tend to buy their own commercial vehicles and there are usually many available options that can be specified at order and fitted during production or changed later. The purpose is to make the finished vehicle more suitable for where it will spend the majority of it's time.

It is usually possible to buy a commercial vehicle with the "wrong" equipment fitted that is still in a proper condition... In my experience it is certainly not unusual to buy one sort of truck and uprate or downrate it in order to qualify for a different rate of taxation.

GM vehicles used to be fitted with a plate embossed with lines of groups of 2, 3 or 4 numbers that are meaningless to most people but when decoded tells the story of the vehicle options fitted to the vehicle - gear ratio, fuel and air filtration, suspension and so forth...
It is best to be guided by those and the chassis number and certainly fit like-for-like unless it is for an approved modification.

http://www.drumhillcycle.com/