1250 x 1250 cnc router (from scratch)

[JAZZCNC]

Does the length of the gantry pose a problem for general machining and would it be able to handle cutting aluminium? As long as the strength is there will it be ok and will the precision still be to a fairly high standard.

Yes Gantry length will greatly affect the machine but not so much for precision but more the quality of finish from machine. Precison or accurecy is down to combination of components and quality of build.
That doesn't mean you can't have long gantry but it does mean it will have to be very strong and substantial to resist resonance and flex which are the enemy of finish quality.
Take this strength to another level if you want to cut Aluminium and achieve good Finish quality. Really unless your only cutting Thin Alu sheet or Profiles etc that don't need good finish then forget cutting Aluminium on such a wide or long moving gantry machine. Yes it will do it but not very well.!!

The support in the Y direction behind the gantry was to mount the motor in the centre with pulleys to the X ballscrews, so didnt really want to add a support the other end as this was to allow material to be fed in / out but if i can position it in a way that the material can be slid under the support i may add this in.

No need One end support will be fine so long the frame is braced well, my machine has this one end setup and it works fine.

If your into wood can I suggest you have the rails slightly overhang the end of bed. Doing this simple thing will give you some nice options easily achieved.
Namely will allow end machining of boards etc for hinges, locks, Dovetails and oversize or oversize awkward parts by clamping to end of machine.
Also if you want a 4th axis makes it very easy to add one see pics for some idea of what I mean.
It's only a cad mock up so pay no attention to details like gantry has thats actually a design I use the other way round it just saved me some drawing time for showing the person it was intended for. It could be used that way round thou.!!