Suspension Set Up

I have just bought a 1998 FSR Elite, frame that I would like to build into a long travel DH Frame, so want to put a modern fork and rear shock.

But I would assume the length of travel in front shock would then mean I need to choose a rear shock to match? Does this make sense or doesn't matter?

Doesn't make sense.
Frame design determines travel. Adding a longer/different shock might just give you an extra 5mm of travel. Or it might simply not fit. That's best case.
Worst case is you'll smash your rear tyre into the frame and lock it up the first time you drop off a kerb. Or break the frame.

At the front end adding longer forks will upset the handling, Jack up the bottom bracket, massively change the weight distribution. (Steeper seattube angle, shorter reach). And if you get carried away the longer lever might rip the head tube off.

Think the fsr was about the 100-120mm travel range depending on model/year. You might go to 130-140 at the front and the back you'll be stuffed unless you can find some new linkages (if they ever even made them). Might struggle to find anything significantly longer travel with a 1 1/8 steerer as well.

So.
You might be able to get away with some minor tweaks to travel. But you'll not make it a long travel DH bike without knackering it. And you don't need to match front and rear travel.

Mattr has explained it pretty well.
No problem in updating to a modern (air) shock and forks as long as the shock eye-to-eye and stroke measurements match the existing shock, and don't go wild with the travel on the front forks.
It's not unusual to have different amounts if travel front/rear, a lot of production bikes are that way, but only by 10-20mm. If you put a 180mm fork on a frame with 100mm rear shock you'll get a very "entertaining" and mostly unpleasant ride !
140mm fork would be good match with the rear shock.

Re:

Thanks for the advice.

I have a modified rear linkage to run a longer rear shock. I will stick to the design of the original length front shock and may be go a bit longer.

You can get long travel linkage plates which up the travel, im sure up to 6". You can run slightly longer on the front. Check a-c length as some forks sit high and like others have said, you dont want to put too much leverage onto the front of the frame. You could also fit a angleset to put the angles back.