SELECT class_union.rn 
FROM (class_okdp,company_with_class AS cwc ,class_user_pk) 
LEFT JOIN  class_okdp cot ON cot.`code` LIKE( CONCAT(class_okdp.code,'%')) 
LEFT JOIN  class_union ON class_union.rn = cot.RN AND class_union.direct=1
LEFT JOIN  company_user_part as cup3 ON cup3.id_company=class_union.id_company AND cup3.id_user=class_union.id_user
WHERE 
  class_user_pk.type_class=2 AND 
  class_user_pk.id_class=class_okdp.RN  AND
  cwc.`code` LIKE CONCAT(class_okdp.code,'%')  AND 
  cwc.direct=0 GROUP BY cwc.id_company,class_okdp.code,cwc.user_union 

Тормоза явно по LEFT JOIN  company_user_part as cup3 ON cup3.id_company=class_union.id_company AND cup3.id_user=class_union.id_user

SELECT class_union.rn, cwc.id_company,class_okdp.code,cwc.user_union
FROM (class_okdp,company_with_class AS cwc ,class_user_pk) 
LEFT JOIN  class_okdp cot ON cot.`code` LIKE( CONCAT(class_okdp.code,'%')) 
LEFT JOIN  class_union ON class_union.rn = cot.RN AND class_union.direct=1
LEFT JOIN  company_user_part as cup3 ON cup3.id_company=class_union.id_company AND cup3.id_user=class_union.id_user
WHERE 
  class_user_pk.type_class=2 AND 
  class_user_pk.id_class=class_okdp.RN  AND
  cwc.`code` LIKE CONCAT(class_okdp.code,'%')  AND 
  cwc.direct=0 GROUP BY cwc.id_company,class_okdp.code,cwc.user_union 

SELECT type_class,
3 as typec, c_union.id_class_user,
IF(cup1.id_global_company_role IS NULL,
1,
cup1.id_global_company_role) as cup1role, 
IF(cup2.id_global_company_role IS NULL,1,cup2.id_global_company_role) as cup2role,
cwc.user_union,
company_with_class.user_union as user_union2, 
company_with_class.id_company, 
company_with_class.id_user AS approve_user, 
user_buyers.nick_user AS nick_approve_user,
cwc.id_company AS gt, 
company_with_class.id_class_union,  
cwc.id_class_union as id_class_union2, 
class_user_pk.id_pk_user AS pk_users, 
cwc.`code_class_user` as code, 
cwc.RN,
cwc.`name_class_user`,
'' AS name2, 
'собственному классификатору' as type1,
3 AS class_type

FROM (company_with_class,company_with_class cwc ,class_user_pk) 
LEFT JOIN  company_user_part as cup1 ON cup1.id_company=company_with_class.id_company AND cup1.id_user=company_with_class.user_union
LEFT JOIN  company_user_part as cup2 ON cup2.id_company=cwc.id_company AND cup2.id_user=cwc.user_union
LEFT JOIN  company as company_buyers on company_buyers.id_company=company_with_class.id_company
LEFT JOIN  user as user_buyers on user_buyers.id_user=company_with_class.id_user
left join class_user_del on company_with_class.code_class_user like concat(class_user_del.code_class_user,'%') and class_user_del.id_user=company_with_class.id_user 
left join class_user_del as cwc_del on cwc.code_class_user like concat(cwc_del.code_class_user,'%') and cwc_del.id_user=cwc.id_user 
LEFT JOIN  class_union AS c_union ON c_union.id_class_union=cwc.id_class_union

WHERE type_class=3 AND class_user_del.id_user IS NULL AND cwc_del.id_user IS NULL AND 
  class_user_pk.id_class=company_with_class.id_class_union  AND  cwc.`code_class_user` LIKE CONCAT(company_with_class.`code_class_user`,'%')  AND
  cwc.direct=0 and company_with_class.direct=1 AND (IsInOkato(company_with_class.id_class_union,cwc.id_class_union))  
GROUP BY cwc.id_company,gt,code,cwc.user_union 

UNION ALL

SELECT type_class,
2 as typec, c_union.id_class_user,
CONCAT(1,',',GROUP_CONCAT( COALESCE( IF(cup3.id_global_company_role IS NULL,1,cup3.id_global_company_role), '0'))  )  as cup1role,
IF(cup2.id_global_company_role IS NULL,1,cup2.id_global_company_role) as cup2role,
cwc.user_union,
4 as user_union2, 
CONCAT(328,',',GROUP_CONCAT( COALESCE(class_union.id_company, '0'))  ) AS id_company, 
CONCAT(4,',',GROUP_CONCAT( COALESCE(class_union.id_user, '0'))  ) AS approve_user,
CONCAT('Администратор',',',GROUP_CONCAT( COALESCE(user_buyers.nick_user, ''))  ) AS nick_approve_user,

cwc.id_company AS gt, 
class_okdp.RN as id_class_union,  
cwc.id_class_union as id_class_union2, 
class_user_pk.id_pk_user AS pk_users, 
cwc.CODE as code, 
cwc.RN,
cwc.`OKDP_NAME`,
'' AS name2, 
'классификатору ОКДП администратора' as type1,
2 AS class_type

FROM (class_okdp,company_with_class cwc ,class_user_pk) 
LEFT join  (class_union, class_okdp cot) ON class_union.rn = cot.RN AND cot.`code` LIKE CONCAT(class_okdp.code,'%') AND class_union.direct=1
LEFT JOIN  company_user_part as cup3 ON cup3.id_company=class_union.id_company AND cup3.id_user=class_union.id_user
LEFT JOIN  company_user_part as cup2 ON cup2.id_company=cwc.id_company AND cup2.id_user=cwc.user_union
LEFT JOIN  company as company_buyers on company_buyers.id_company=class_union.id_company
LEFT JOIN  user as user_buyers on user_buyers.id_user=class_union.id_user
LEFT JOIN  class_union AS c_union ON c_union.id_class_union=cwc.id_class_union

WHERE type_class=2 AND class_user_pk.id_class=class_okdp.RN  AND  cwc.`code` LIKE CONCAT(class_okdp.code,'%')  AND 
  cwc.direct=0
GROUP BY cwc.id_company,gt,code,cwc.user_union