Help optimising my complex mysql query

I'm trying to extract some data from a pretty large mySQL database for a report. I've got most of what I want, but when I add in an extra level of detail, my query takes too long to run. Here is the SQL: I've already rewritten it to take out the JOIN syntax and I've got indexes on the parts I am using:

SELECT o.name, o.id, c.name, c.id as cid, box.site_id as siteid
, (select count(bf.id)
FROM batches b, batchfile bf, files f, boxes bo  
where
bf.batch_id = b.id
and bf.file_id = f.id
and f.box_id = bo.id
and b.batchtype = 0 and b.requestDate between '2014-03-01' and '2015-03-01' and b.client_id = cid and ((siteid is null and bo.site_id is null) or (bo.site_id = siteid))) as 'file deposits'
FROM boxes box, clients c, organisations o, batches b, batchfile bf, files f
where bf.batch_id = b.id
and bf.file_id = f.id
and f.box_id = box.id
and b.client_id = c.id
and c.organisation_id = o.id
and b.requestDate between '2014-03-01' and '2015-03-01'
and batchtype = 0
group by siteid, c.id;

Explain query gives me this:
1      PRIMARY      b      range      PRIMARY,FKEC39FD68A2287183,requestDate,batchtype,id_requestDate,idx_requestYear,batchtype_requestDate      batchtype_requestDate      10            2302      Using where; Using temporary; Using filesort
1      PRIMARY      c      eq_ref      PRIMARY,FK334B86089EC80063      PRIMARY      8      fileexpress.b.client_id      1      
1      PRIMARY      o      eq_ref      PRIMARY      PRIMARY      8      fileexpress.c.organisation_id      1      
1      PRIMARY      bf      ref      FKC5B09FB681F11E23,FKC5B09FB682CEBEB1      FKC5B09FB682CEBEB1      9      fileexpress.b.id      8      Using where
1      PRIMARY      f      eq_ref      PRIMARY,FK5CEBA77DCAF4AD1      PRIMARY      8      fileexpress.bf.file_id      1      
1      PRIMARY      box      eq_ref      PRIMARY      PRIMARY      8      fileexpress.f.box_id      1      
2      DEPENDENT SUBQUERY      b      ref      PRIMARY,FKEC39FD68A2287183,requestDate,batchtype,id_requestDate,idx_requestYear,batchtype_requestDate      FKEC39FD68A2287183      9      func      25      Using where
2      DEPENDENT SUBQUERY      bf      ref      FKC5B09FB681F11E23,FKC5B09FB682CEBEB1      FKC5B09FB682CEBEB1      9      fileexpress.b.id      8      Using where
2      DEPENDENT SUBQUERY      f      eq_ref      PRIMARY,FK5CEBA77DCAF4AD1      PRIMARY      8      fileexpress.bf.file_id      1      
2      DEPENDENT SUBQUERY      bo      eq_ref      PRIMARY,FK59943B93218C643,site_id      PRIMARY      8      fileexpress.f.box_id      1      Using where

Any help would be greatly appreciated. I feel as if I'm missing something really obvious and stupid :-(

many thanks!